Haplotypes
Polymorphism, Single Nucleotide
Linkage Disequilibrium
Gene Frequency
Alleles
Polymorphism, Genetic
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
Genotype
Genetic Predisposition to Disease
Genetics, Population
DNA, Mitochondrial
Genetic Markers
Sequence Analysis, DNA
Founder Effect
A phenomenon that is observed when a small subgroup of a larger POPULATION establishes itself as a separate and isolated entity. The subgroup's GENE POOL carries only a fraction of the genetic diversity of the parental population resulting in an increased frequency of certain diseases in the subgroup, especially those diseases known to be autosomal recessive.
Case-Control Studies
Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group.
HLA-DQ Antigens
Microsatellite Repeats
Chromosome Mapping
Genetic Linkage
Polymorphism, Restriction Fragment Length
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
HLA-DRB1 Chains
Models, Genetic
Pedigree
European Continental Ancestry Group
Base Sequence
HLA-DR Antigens
HLA Antigens
Asian Continental Ancestry Group
Major Histocompatibility Complex
The genetic region which contains the loci of genes which determine the structure of the serologically defined (SD) and lymphocyte-defined (LD) TRANSPLANTATION ANTIGENS, genes which control the structure of the IMMUNE RESPONSE-ASSOCIATED ANTIGENS, HUMAN; the IMMUNE RESPONSE GENES which control the ability of an animal to respond immunologically to antigenic stimuli, and genes which determine the structure and/or level of the first four components of complement.
Geography
Evolution, Molecular
Genetic Association Studies
Phylogeography
Y Chromosome
HLA-DR3 Antigen
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Genes, MHC Class II
Phenotype
HLA-B Antigens
Class I human histocompatibility (HLA) surface antigens encoded by more than 30 detectable alleles on locus B of the HLA complex, the most polymorphic of all the HLA specificities. Several of these antigens (e.g., HLA-B27, -B7, -B8) are strongly associated with predisposition to rheumatoid and other autoimmune disorders. Like other class I HLA determinants, they are involved in the cellular immune reactivity of cytolytic T lymphocytes.
Heterozygote
Recombination, Genetic
Cytochromes b
Chromosomes, Human, Y
Bahrain
An independent state, an archipelago in the western Persian Gulf, northwest of Qatar. It comprises low-lying islands of Bahrain (the largest), Muharraq, Sitra, and several islets. It has extensive oil fields. The name comes from the Arabic al-bahrayn, "the two seas", with reference to its lying in the middle of a bay with its "two seas" east and west of it. (From Webster's New Geographical Dictionary, 1988, p107 & Room, Brewer's Dictionary of Names, 1992, p45)
Mutation
African Continental Ancestry Group
HLA-B8 Antigen
HLA-A Antigens
Polymorphic class I human histocompatibility (HLA) surface antigens present on almost all nucleated cells. At least 20 antigens have been identified which are encoded by the A locus of multiple alleles on chromosome 6. They serve as targets for T-cell cytolytic responses and are involved with acceptance or rejection of tissue/organ grafts.
Gene Pool
Polynesia
The collective name for the islands of the central Pacific Ocean, including the Austral Islands, Cook Islands, Easter Island, HAWAII; NEW ZEALAND; Phoenix Islands, PITCAIRN ISLAND; SAMOA; TONGA; Tuamotu Archipelago, Wake Island, and Wallis and Futuna Islands. Polynesians are of the Caucasoid race, but many are of mixed origin. Polynesia is from the Greek poly, many + nesos, island, with reference to the many islands in the group. (From Webster's New Geographical Dictionary, 1988, p966 & Room, Brewer's Dictionary of Names, 1992, p426)
Likelihood Functions
Genes, MHC Class I
Promoter Regions, Genetic
Selection, Genetic
Genetic Loci
Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.
Algorithms
Gene Flow
HLA-A1 Antigen
DNA
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Ethnic Groups
Indians, South American
Exons
Species Specificity
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
DNA Primers
Risk Factors
Genome, Human
Asia
The largest of the continents. It was known to the Romans more specifically as what we know today as Asia Minor. The name comes from at least two possible sources: from the Assyrian asu (to rise) or from the Sanskrit usa (dawn), both with reference to its being the land of the rising sun, i.e., eastern as opposed to Europe, to the west. (From Webster's New Geographical Dictionary, 1988, p82 & Room, Brewer's Dictionary of Names, 1992, p34)
Introns
Diabetes Mellitus, Type 1
A subtype of DIABETES MELLITUS that is characterized by INSULIN deficiency. It is manifested by the sudden onset of severe HYPERGLYCEMIA, rapid progression to DIABETIC KETOACIDOSIS, and DEATH unless treated with insulin. The disease may occur at any age, but is most common in childhood or adolescence.
HLA-C Antigens
Class I human histocompatibility (HLA) antigens encoded by a small cluster of structural genes at the C locus on chromosome 6. They have significantly lower immunogenicity than the HLA-A and -B determinants and are therefore of minor importance in donor/recipient crossmatching. Their primary role is their high-risk association with certain disease manifestations (e.g., spondylarthritis, psoriasis, multiple myeloma).
Receptors, KIR
A family of receptors found on NK CELLS that have specificity for a variety of HLA ANTIGENS. KIR receptors contain up to three different extracellular immunoglobulin-like domains referred to as D0, D1, and D2 and play an important role in blocking NK cell activation against cells expressing the appropriate HLA antigens thus preventing cell lysis. Although they are often referred to as being inhibitory receptors, a subset of KIR receptors may also play an activating role in NK cells.
Biological Evolution
Phenylketonurias
A group of autosomal recessive disorders marked by a deficiency of the hepatic enzyme PHENYLALANINE HYDROXYLASE or less frequently by reduced activity of DIHYDROPTERIDINE REDUCTASE (i.e., atypical phenylketonuria). Classical phenylketonuria is caused by a severe deficiency of phenylalanine hydroxylase and presents in infancy with developmental delay; SEIZURES; skin HYPOPIGMENTATION; ECZEMA; and demyelination in the central nervous system. (From Adams et al., Principles of Neurology, 6th ed, p952).
Siberia
Inheritance Patterns
Steroid 21-Hydroxylase
An adrenal microsomal cytochrome P450 enzyme that catalyzes the 21-hydroxylation of steroids in the presence of molecular oxygen and NADPH-FERRIHEMOPROTEIN REDUCTASE. This enzyme, encoded by CYP21 gene, converts progesterones to precursors of adrenal steroid hormones (CORTICOSTERONE; HYDROCORTISONE). Defects in CYP21 cause congenital adrenal hyperplasia (ADRENAL HYPERPLASIA, CONGENITAL).
Genome-Wide Association Study
Tandem Repeat Sequences
Haploidy
Histocompatibility Testing
Identification of the major histocompatibility antigens of transplant DONORS and potential recipients, usually by serological tests. Donor and recipient pairs should be of identical ABO blood group, and in addition should be matched as closely as possible for HISTOCOMPATIBILITY ANTIGENS in order to minimize the likelihood of allograft rejection. (King, Dictionary of Genetics, 4th ed)
Association of polymorphism at the type I collagen (COL1A1) locus with reduced bone mineral density, increased fracture risk, and increased collagen turnover. (1/12035)
OBJECTIVE: To examine the relationship between a common polymorphism within intron 1 of the COL1A1 gene and osteoporosis in a nested case-control study. METHODS: We studied 185 healthy women (mean +/- SD age 54.3+/-4.6 years). Bone mineral density (BMD) was measured using dual x-ray absorptiometry, and fractures were determined radiographically. The COL1A1 genotype was assessed using the polymerase chain reaction and Bal I endonuclease digestion. RESULTS: Genotype frequencies were similar to those previously observed and in Hardy-Weinberg equilibrium: SS 61.1%, Ss 36.2%, and ss 2.7%. Carriage of at least one copy of the "s" allele was associated with a significant reduction in lumbar spine BMD (P = 0.02) and an increased risk of total fracture (P = 0.04). Urinary pyridinoline levels were significantly elevated in those with the risk allele (P < 0.05). CONCLUSION: These data support the findings that the COL1A1 gene polymorphism is associated with low BMD and fracture risk, and suggest a possible physiologic effect on total body turnover of type I collagen. (+info)A novel method for determining linkage between DNA sequences: hybridization to paired probe arrays. (2/12035)
Cooperative hybridization has been used to establish physical linkage between two loci on a DNA strand. Linkage was detected by hybridization to a new type of high-density oligonucleotide array. Each synthesis location on the array contains a mixture of two different probe sequences. Each of the two probes can hybridize independently to a different target sequence, but if the two target sequences are physically linked there is a cooperative increase in hybridization yield. The ability to create and control non-linear effects raises a host of possibilities for applications of oligonucleotide array hybridization. The method has been used to assign linkage in 50:50 mixtures of DNA containing single nucleotide polymorphisms (SNPs) separated by 17, 693, 1350 and 2038 bp and to reconstruct haplotypes. Other potential uses include increasing the specificity of hybridization in mutation detection and gene expression monitoring applications, determining SNP haplotypes, characterizing repetitive sequences, such as short tandem repeats, and aiding contig assembly in sequen-cing by hybridization. (+info)The haplotype distribution of two genes of citrus tristeza virus is altered after host change or aphid transmission. (3/12035)
Genetic variability of citrus tristeza virus (CTV) was studied using the haplotypes detected by single-strand conformation polymorphism (SSCP) analysis of genes p18 and p20 in six virus populations of two origins. The Spanish group included a CTV isolate and subisolates obtained by graft-transmission to different host species. The other included two subisolates aphid-transmitted from a single Japanese isolate. The homozygosity observed for gene p20 was always significantly higher than that expected under neutral evolution, whereas only three populations showed high homozygosity for p18, suggesting stronger host constraints for p20 than for p18. Sequential transmissions of a Spanish isolate to new host species increased the difference between its population and that of the successive subisolates for gene p18, as estimated by the F statistic. Analysis of molecular variance indicated that variation between both groups of populations was not statistically significant, whereas variations between populations of the same group or within populations were significant for both genes studied. Our data indicate that selection affects the haplotype distribution and that adaptation to a new host can be as important or more as the geographical origin. Variation of the CTV populations after host change or aphid transmission may explain in part the wide biological variability observed among CTV isolates. (+info)DYT1 mutation in French families with idiopathic torsion dystonia. (4/12035)
A GAG deletion at position 946 in DYT1, one of the genes responsible for autosomal dominant idiopathic torsion dystonia (ITD), has recently been identified. We tested 24 families and six isolated cases with ITD and found 14 individuals from six French families who carried this mutation, indicating that 20% of the affected families carried the DYT1 mutation. Age at onset was always before 20 years (mean, 9+/-4 years). Interestingly, the site of onset was the upper limb in all but one patient. Dystonia was generalized in seven patients and remained focal or segmental in three patients. The absence of common haplotypes among DYT1 families suggests that at least six independent founder mutations have occurred. In addition, one Ashkenazi Jewish family carried the common haplotype described previously in Ashkenazi Jewish patients, but it was absent in the other family. Moreover, the dystonia remained focal in the latter family when compared with the usual generalized phenotype in patients with the common Ashkenazi Jewish haplotype. This indicates that there are at least two founder mutations in this population. (+info)A common MSH2 mutation in English and North American HNPCC families: origin, phenotypic expression, and sex specific differences in colorectal cancer. (5/12035)
The frequency, origin, and phenotypic expression of a germline MSH2 gene mutation previously identified in seven kindreds with hereditary non-polyposis cancer syndrome (HNPCC) was investigated. The mutation (A-->T at nt943+3) disrupts the 3' splice site of exon 5 leading to the deletion of this exon from MSH2 mRNA and represents the only frequent MSH2 mutation so far reported. Although this mutation was initially detected in four of 33 colorectal cancer families analysed from eastern England, more extensive analysis has reduced the frequency to four of 52 (8%) English HNPCC kindreds analysed. In contrast, the MSH2 mutation was identified in 10 of 20 (50%) separately identified colorectal families from Newfoundland. To investigate the origin of this mutation in colorectal cancer families from England (n=4), Newfoundland (n=10), and the United States (n=3), haplotype analysis using microsatellite markers linked to MSH2 was performed. Within the English and US families there was little evidence for a recent common origin of the MSH2 splice site mutation in most families. In contrast, a common haplotype was identified at the two flanking markers (CA5 and D2S288) in eight of the Newfoundland families. These findings suggested a founder effect within Newfoundland similar to that reported by others for two MLH1 mutations in Finnish HNPCC families. We calculated age related risks of all, colorectal, endometrial, and ovarian cancers in nt943+3 A-->T MSH2 mutation carriers (n=76) for all patients and for men and women separately. For both sexes combined, the penetrances at age 60 years for all cancers and for colorectal cancer were 0.86 and 0.57, respectively. The risk of colorectal cancer was significantly higher (p<0.01) in males than females (0.63 v 0.30 and 0.84 v 0.44 at ages 50 and 60 years, respectively). For females there was a high risk of endometrial cancer (0.5 at age 60 years) and premenopausal ovarian cancer (0.2 at 50 years). These intersex differences in colorectal cancer risks have implications for screening programmes and for attempts to identify colorectal cancer susceptibility modifiers. (+info)Analysis of spinocerebellar ataxia type 2 gene and haplotype analysis: (CCG)1-2 polymorphism and contribution to founder effect. (6/12035)
Spinocerebellar ataxia type 2 is a familial spinocerebellar ataxia with autosomal dominant inheritance. The gene responsible was recently cloned and this disorder was found to be the result of a CAG expansion in its open reading frame. We analysed 13 SCA2 patients in seven unrelated families in Gunma Prefecture, Japan. In four of the seven families, we detected CCG or CCGCCG interruptions in only the expanded alleles. Cosegregation of these polymorphisms with SCA2 patients was established within each family. Together with the results of haplotype analyses, we considered that at least two founders were present in our area and that these (CCG)1-2 polymorphisms may make analysis of founder effects easier. By sequencing analysis we found that although the number of the long CAG repeat varied in each subclone of expanded alleles, these polymorphisms did not change their configuration. This finding suggests that CCG or CCGCCG sequences are stable when surrounded by the long CAG repeat and a single CAG. Moreover, the presence of these polymorphisms may lead to miscounting the repeat size by conventional estimation using a size marker such as an M13 sequencing ladder. Therefore we should consider these polymorphisms and accurately determine the repeat size by sequencing. (+info)Der(22) syndrome and velo-cardio-facial syndrome/DiGeorge syndrome share a 1.5-Mb region of overlap on chromosome 22q11. (7/12035)
Derivative 22 (der[22]) syndrome is a rare disorder associated with multiple congenital anomalies, including profound mental retardation, preauricular skin tags or pits, and conotruncal heart defects. It can occur in offspring of carriers of the constitutional t(11;22)(q23;q11) translocation, owing to a 3:1 meiotic malsegregation event resulting in partial trisomy of chromosomes 11 and 22. The trisomic region on chromosome 22 overlaps the region hemizygously deleted in another congenital anomaly disorder, velo-cardio-facial syndrome/DiGeorge syndrome (VCFS/DGS). Most patients with VCFS/DGS have a similar 3-Mb deletion, whereas some have a nested distal deletion endpoint resulting in a 1.5-Mb deletion, and a few rare patients have unique deletions. To define the interval on 22q11 containing the t(11;22) breakpoint, haplotype analysis and FISH mapping were performed for five patients with der(22) syndrome. Analysis of all the patients was consistent with 3:1 meiotic malsegregation in the t(11;22) carrier parent. FISH-mapping studies showed that the t(11;22) breakpoint occurred in the same interval as the 1.5-Mb distal deletion breakpoint for VCFS. The deletion breakpoint of one VCFS patient with an unbalanced t(18;22) translocation also occurred in the same region. Hamster-human somatic hybrid cell lines from a patient with der(22) syndrome and a patient with VCFS showed that the breakpoints occurred in an interval containing low-copy repeats, distal to RANBP1 and proximal to ZNF74. The presence of low-copy repetitive sequences may confer susceptibility to chromosome rearrangements. A 1.5-Mb region of overlap on 22q11 in both syndromes suggests the presence of dosage-dependent genes in this interval. (+info)Location score and haplotype analyses of the locus for autosomal recessive spastic ataxia of Charlevoix-Saguenay, in chromosome region 13q11. (8/12035)
Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a clinically homogeneous form of early-onset familial spastic ataxia with prominent myelinated retinal nerve fibers. More than 300 patients have been identified, and most of their families originated in the Charlevoix-Saguenay region of northeastern Quebec, where the carrier prevalence has been estimated to be 1/22. Consistent with the hypothesis of a founder effect, we observed excess shared homozygosity at 13q11, among patients in a genomewide scan of 12 families. Analysis of 19 pedigrees demonstrated very tight linkage between the ARSACS locus and an intragenic polymorphism of the gamma-sarcoglycan (SGCG) gene, but genomic DNA sequence analysis of all eight exons of SGCG revealed no disease-causing mutation. On the basis of haplotypes composed of seven marker loci that spanned 11.1 cM, the most likely position of the ARSACS locus was 0.42 cM distal to the SGCG polymorphism. Two groups of ARSACS-associated haplotypes were identified: a large group that carries a common SGCG allele and a small group that carries a rare SGCG allele. The haplotype groups do not appear to be closely related. Therefore, although chromosomes within each haplotype group may harbor a single ARSACS mutation identical by descent, the two mutations could have independent origins. (+info)
TNF block haplotypes reveal diverse pathways between TNF and disease: Implications for understanding neuropathy in HIV patients
Direct analysis of unphased SNP genotype data in population-based association studies via Bayesian partition modelling of...
CRAN Task View: Statistical Genetics
CRAN Task View: Statistical Genetics
Association of extended interleukin-10 promoter haplotypes with disease susceptibility and manifestations in German patients...
Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. - Oxford Neuroscience
Genotype-phenotype analysis of the Crohns disease susceptibility haplotype on chromosome 5q31
A fast algorithm for genome-wide haplotype pattern mining | BMC Bioinformatics | Full Text
HaploRec: efficient and accurate large-scale reconstruction of haplotypes | BMC Bioinformatics | Full Text
Unique TCR beta-subunit variable gene haplotypes in Africans. - Nuffield Department of Medicine
Making a haplotype catalog with estimated frequencies based on SNP homozygotes<...
Plus it
rs1048661 - SNPedia
Complex SNP-based haplotypes in three human helicases: Implications for cancer association studies<...
MHC haplotypes modulate strength of natural killer (NK) cell licensing (91.10) | The Journal of Immunology
Haplogroup - Metapedia
BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads | Genome Biology | Full Text
Molecular phylogenetics - Wikipedia
Alt Haplotypes Track Settings
Alt Haplotypes Track Settings
Alt Haplotypes Track Settings
Alt Haplotypes Track Settings
HaploPOP : a software that improves population assignment by combining markers into haplotypes
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested...
MtDNA diversity and species phylogeny of western Palaearctic members of the Gerris lacustris group (Hemiptera-Heteroptera:...
Lack of association between four SNPs in the SLC22A3-LPAL2-LPA gene cluster and coronary artery disease in a Chinese Han...
Book Algorithms for Haplotype Inference and Block Partitioning: Perfect Phylogeny Based Approaches for the Haplotype Inference...
A New Statistic for Detecting Genetic Differentiation | Genetics
A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors
Analysis of the functional role of interleukin-6 promoter haplotype in a macrophage cell model - Surrey Research Insight Open...
Plus it
Haplotype structure and selection of the MDM2 oncogene in humans - CSHL Scientific Digital Repository
HAPLOTYPE STUDY OF THE CYP4A11 GENE AND CORONARY ARTERY DISEASE IN A HAN AND A UYGUR POPULATION OF CHINA | Heart
New hope for haplotype mapping | Arthritis Research & Therapy | Full Text
Genotypes and haplotypes in the insulin-like growth factors, their receptors and binding proteins in relation to plasma...
Four common HLA haplotypes and their association with diseases in the Japanese population<...
SNP survey finds surprising similarity in humans worldwide
Haplotype-assisted genomic evaluations in Nordic Red dairy cattle | WCGALP Archive
Brevet US7615350 - Methods for haplotyping genomic DNA - Google Brevets
Haplotype Diversity
How do we interpret a rooted haplotype network?
How do we interpret a rooted haplotype network?
Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus | PNAS
JCI -
Increased expression of anion transporter SLC26A9 delays diabetes onset in cystic fibrosis
Mapping-free variant calling using haplotype reconstruction from k-mer frequencies, Bioinformatics | 10.1093/bioinformatics...
MDR1/ABCB1 gene polymorphisms in patients with chronic myeloid leukemia
HapIso - ZarLab
Dienekes Anthropology Blog: New paper on Y chromosome haplogroup T
Dienekes Anthropology Blog: New paper on Y chromosome haplogroup T
Mitochondrial DNA Polymorphism, Maternal Lineage and Correlations with Postnatal Growth of Japanese Black Beef Cattle to...
Mitochondrial Haplogroups | Circulation
Mitochondrial DNA haplogroups and ageing mechanisms in osteoarthritis | Annals of the Rheumatic Diseases
Haplogroup L1 (mtDNA) - Wikipedia
Efficient mining of haplotype patterns for linkage disequilibrium mapp by Lin L., Wong L. et al.
Positive association of the human GABA-A-receptor beta 2 subunit gene haplotype with schizophrenia in the Chinese Han...
Survival and mitochondrial function in septic patients according to mitochondrial DNA haplogroup | Critical Care | Full Text
Linkage disequilibrium blocks, haplotype structure, and htSNPs of human CYP7A1 gene
Genetic architecture of trout from Albania as revealed by mtDNA control region variation - omicX
An investigation of 10 Y-STR loci and the detection of specific haplotype frequencies in Turkish population
Abstract P259: Functional Characterization of an ALOX15 Promoter Variant Associated with Coronary Artery Calcification:...
Y-chromosome STR haplotypes in Córdoba (Argentina). - Semantic Scholar
Research of single mitochondrial nucleotide substitutions in male infertility should consider human mitochondrial haplogroups -...
Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity...
The identification and characterization of alleles of sucrose phosphat by C Lynne McIntyre, Mark Jackson et al.
Identification of a cryptic lethal mutation in the mouse t(w73) haplot by G R. Howell, R A. Bergstrom et al.
An Improved Version of Logistic Bayesian Lasso for Detecting Rare Haplotype-Environment Interactions with Application to Lung...
Haplotype - Wikipedia
Single nucleotide polymorphisms in the human interleukin-1B gene affect transcription according to haplotype context : Human...
Fine-scale spatial and temporal dynamics of kdr haplotypes in Aedes aegypti from Mexico | Parasites & Vectors | Full Text
Genotype imputation using the Positional Burrows Wheeler Transform. - Wellcome Centre for Human Genetics
Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters
Plus it
Estimating KIR Haplotype Frequencies on a Cohort of 10,000 Individuals: A Comprehensive Study on Population Variations, Typing...
Project MUSE - Mitochondrial DNA Sequence Variation in the Boyko, Hutsul, and Lemko Populations of the Carpathian Highlands
Functional promoter haplotypes of the human FAS gene are associated with the phenotype of SLE characterized by thrombocytopenia
Lack of Association between Y-Chromosomal Haplogroups and Prostate Cancer in the Korean Population
Increased in vivo transcription of an IL-8 haplotype associated with respiratory syncytial virus disease-susceptibility. -...
Statistical distributions of test statistics used for quantitative trait association mapping in structured populations |...
A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the...
Linkage disequilibrium mapping via cladistic analysis of SNP haplotypes. - Wellcome Centre for Human Genetics
Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus - Nottingham ePrints
A reference panel of 64,976 haplotypes for genotype imputation. - Oxford Cardiovascular Science
Haplotypic structure of the X chromosome in the COGA population sample and the quality of its reconstruction by extant software...
Human cytochrome P450 2B6 genetic variability in Botswana: a case of haplotype diversity and convergent phenotypes
IJMS | Free Full-Text | Association Study between BDNF Gene Polymorphisms and Autism by Three-Dimensional Gel-Based Microarray
Impact of migration and fitness on the stability of lethal t-haplotype by Dannie Durand, Kristin Ardlie et al.
Origin Hunters - Genetic Genealogist: 2015
Origin Hunters - Genetic Genealogist: January 2015
Networks of STR haplotypes based on penta- and hexanucl | Open-i
Genetyp-phenotype association studies in clinically well characterized patients with inherited bleeding disorders
Human leukocyte antigen
Haplotypes[edit]. An HLA haplotype is a series of HLA "genes" (loci-alleles) by chromosome, one passed from the mother and one ... Haplotypes can be obtained by typing family members in areas of the world where SSP-PCR is unable to recognize alleles and ... These haplotypes can be used to trace migrations in the human population because they are often much like a fingerprint of an ... The Super-B8 haplotype is enriched in the Western Irish, declines along gradients away from that region, and is found only in ...
Talk:Haplogroup R-M167
Haplotypes[edit]. Modal[edit]. *R1b1b2a1a2c Modal Haplotype. Ysearch 77ADS. DYS. 393. 390. 19. 391. 385A. 385B. 426. 388. 439. ... This is my paternal haplotype. I don't know how it ended up on this Wikipedia article. All I know is that my earliest known ... If all Your 25 markers are identical with the above, it means that You have a modal haplotype of Your haplogroup. However, many ... people have the modal haplotype. YOMAL SIDOROFF-BIARMSKII (talk) 19:17, 13 August 2013 (UTC). New Research Articles[edit]. ...
Family Tree DNA
Their haplotypes matched perfectly. Cite journal requires ,journal= (help) Gibbens, Pam (April 2006). "Talk of The Town - At ... Michael Hammer (PhD), one of a team of scientists that first published on the Cohen Modal Haplotype in 1997 in the journal ... FamilyTreeDNA became widely known for its Y-chromosome STR testing for the Cohen Modal Haplotype. Soon, they were offering not ...
Genealogical DNA test
... with Y-STR values clustered unusually closely around a haplotype known as the Cohen Modal Haplotype (CMH). This could be ... Their haplotypes matched perfectly. Cite journal requires ,journal= (help) Lomax, John Nova (14 April 2005). "Who's Your Daddy ... "Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood". Human Genetics. 126 (5): 707- ...
Nanopore sequencing
Ammar R, Paton TA, Torti D, Shlien A, Bader GD (2015). "CYP2D6 variants and haplotypes". F1000Research. 4: 17. doi:10.12688/ ... haplotyping and other applications. Nanopore sequencing took 25 years to fully materialise. It involved close collaboration ...
Genetic genealogy
Their haplotypes matched perfectly. Cite journal requires ,journal= (help) Lomax, John Nova (April 14, 2005). "Who's Your Daddy ... "The impact of additional Y-STR loci on resolving common haplotypes and closely related individuals". Forensic Science ... Electropherogram Family name Forensic genealogy Genealogical DNA test Genealogy Genetic recombination Haplogroup Haplotype ...
Haplogroup J (Y-DNA)
2001, see Modal Haplotypes of "J1" (as Eu10) Sanchez, Juan J; Hallenberg, Charlotte; Børsting, Claus; Hernandez, Alexis; Gorlin ... Moreover, the network analysis of J-P58 haplotypes shows that some of the populations with low diversity, such as Bedouins from ... Jobling, Mark A.; Tyler-Smith, Chris (2000). "New uses for new haplotypes". Trends in Genetics. 16 (8): 356-62. doi:10.1016/ ... yJdb: the Y-haplogroup J database haplotypes of haplogroup J. [1] Haplogroup J subclades at International Society of Genetic ...
Takabuti
"Haplotyping Takabuti". KNH Centre for Biomedical Egyptology. Retrieved 2021-01-13. Drosou, Konstantina; Collin, Thomas C.; ... Freeman, Peter J.; Loynes, Robert; Freemont, Tony (2020-10-12). "The first reported case of the rare mitochondrial haplotype ...
Allele
"What are variants, alleles and haplotypes? , Human genetic variation". Retrieved 16 November 2020. Seltsam A, Hallensleben M, ...
Self-incompatibility
"The S haplotype-specific F-box protein gene, SFB, is defective in self-compatible haplotypes of Prunus avium and P. mume". ... The units are called S-haplotypes. The translation products of the two regions of the S-locus are two proteins which, by ... However, when a female determinant interacts with a male determinant of a different haplotype, no SI is created, and ... There are possibly up to 100 polymorphs of the S-haplotype in Brassica, and within these there is a dominance hierarchy. The ...
Ann T. Bowling
Bowling, AT; Scott, AM; Flint, J; Clegg, JB (1988). "Novel alpha haemoglobin haplotypes in horses". Animal Genetics. 19 (2): 87 ...
Andamanese peoples
2001) as M4 and M2 ... The Andamanese M2 contains two haplotypes ... developed in situ, after an early colonization ... ... The Andaman M4 haplotype ... is still present among populations in India, suggesting it was subject to the late Pleistocene ... Alternatively, it is possible that the haplotypes have become extinct in India or are present at a low frequency and have not ...
HLA-DQ6
There are many haplotypes of DQ6. DQB1*0601 is generally linked to DQA1*0103 as 6.1 haplotype. This haplotype is more common in ... This haplotype is considered to be the longest multigene haplotype known within the human genome as it covers over 4.7 million ... The DR15-DQ6.2 haplotype is the most common DR-DQ haplotype in Europe, and approximately 30% of Americans carry at least DQ6.2 ... This haplotype is found at its highest Eurasian frequencies in Japan. DQB1*0609 is found in Africa and proximal regions of ...
Variants of SARS-CoV-2
"Global Report Investigating Novel Coronavirus Haplotypes". cov-lineages.org. Pango team. "Living Evidence - SARS-CoV-2 variants ...
Tag SNP
This measure is suitable only for haplotype blocks with limited haplotype diversity and it is not clear how to use it for large ... When a disease is found to be associated with a haplotype, some SNPs in that haplotype will have synthetic association with the ... Therefore, tag SNPs are representative of all SNPs within a haplotype. The selection of tag SNPs is dependent on the haplotypes ... By mapping the entire genome to haplotypes, tag SNPs can be identified to represent the haplotype blocks examined by genetic ...
Apolipoprotein A1
Lately,[when?] two novel susceptibility haplotypes i.e. P2-S2-X1 and P1-S2-X1 have been discovered in ApoAI-CIII-AIV gene ...
Semisulcospira libertina
2013) studied mitochondrial haplotypes of Semisulcospira libertina from Korea and from Japan. Mixed haplotypes in Korea suggest ... mitochondrial haplotypes have Japanese sister lineages". Journal of Molluscan Studies. 79 (1): 86-89. doi:10.1093/mollus/eys036 ...
Haplogroup T-M184
Rapone C, Geraci A, Capelli C, De Meo A, D'Errico G, Barni F, Berti A, Lago G (2007). "Y chromosome haplotypes in Central-South ... Melo MM, Carvalho M, Lopes V, Anjos MJ, Serra A, Vieira DN, Sequeiros J, Corte-Real F (2011). "Y-STR haplotypes in three ethnic ... 2012). "Haplotype diversity of 17 Y-str loci in an admixed population from the Brazilian Amazon". Genetics and Molecular ... Sánchez C, Barrot C, Xifró A, Ortega M, de Aranda IG, Huguet E, Corbella J, Gené M (2007). "Haplotype frequencies of 16 Y- ...
Endothelial NOS
Haplotypes including the SNPs g.-786T>C and Glu298Asp and the VNTR in intron 4 affected the susceptibility to hypertension, ... Souza-Costa DC, Belo VA, Silva PS, Sertorio JT, Metzger IF, Lanna CM, Machado MA, Tanus-Santos JE (Mar 2011). "eNOS haplotype ... Sandrim VC, de Syllos RW, Lisboa HR, Tres GS, Tanus-Santos JE (Nov 2006). "Endothelial nitric oxide synthase haplotypes affect ... In addition to analysis of genetic polymorphisms individually, haplotypes including the SNPs g.-786T>C and Glu298Asp and the ...
Ancient Egyptian race controversy
Diversity of 17-locus Y-STR haplotypes in Upper (Southern) Egyptians Ghada A. Omran, Guy N. Rutty, Mark A. Jobling, 2007, ... Lucotte, G.; Mercier, G. (2003). "Brief communication: Y-chromosome haplotypes in Egypt". American Journal of Physical ... "A Back Migration from Asia to Sub-Saharan Africa is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes". ...
DNA history of Egypt
Haplotype V is common in Berbers and has a low frequency outside North Africa. Haplotypes V, XI, and IV are all predominantly ... Lucotte G, Mercier G (May 2003). "Brief communication: Y-chromosome haplotypes in Egypt". American Journal of Physical ... Underhill (2002), Bellwood and Renfrew, ed., Inference of Neolithic Population Histories using Y-chromosome Haplotypes, ... characterized by a high M1 haplotype frequency and a comparatively low L1 and L2 macrohaplogroup frequency of 20.6%. Another ...
Vasopressin receptor 1A
"Musical aptitude is associated with AVPR1A-haplotypes". PLOS ONE. 4 (5): e5534. doi:10.1371/journal.pone.0005534. PMC 2678260. ...
Gluten immunochemistry
The HLA-A antigens can mediate apoptosis in autoimmune disease and HLA A*0201 in with the HLA-DQ8 haplotypes has been ... Understanding DQ Haplotypes and DQ isoforms on the right). HLA-DQ2 primarily presents gliadins with the HLA-DQ isoform DQ2.5 ( ... Understanding DQ haplotypes and DQ isoforms). HLA-DQ8 is generally not as involved in the most severe complications, and it ... see Understanding DQ haplotypes and DQ isoforms on the right) However, numbers of different proteins from the grass tribe ...
Mark Stoneking
HLA-DQ haplotypes in 15 different populations. In: The Major Histocompatibility Complex: Evolution, Structure and Function. M ... "Recent positive selection of a human androgen receptor/ectodysplasin A2 receptor haplotype and its relationship to male pattern ...
Amphiprion akindynos
There were no shared haplotypes between species. A. akindynos (Barrier Reef anemonefish) A. clarkii (Clark's anemonefish) A. ...
Amphiprion mccullochi
There were no shared haplotypes between species. A. mccullochi (Whitesnout anemonefish) A. melanopus (Red & Black anemonefish) ...
Hequ horse
Six haplotypes were identified in horses Gansu. Cluster E is only present in the Hequ, which probably has the same origin as ...
Polynesian Dog
... "the dingo founder haplotype" A29 (8%). Also present were haplotypes A120 and A145. All 4 haplotypes fall within the a2 mDNA sub ... This short haplotype was named Arc2 and corresponds to mDNA haplotypes A75 and A120, and it could be found in 70% of samples ... The study of mtDNA show they carried two haplotypes: Arc1 and Arc2. In 2011, the mDNA of dogs from the Malay Peninsula found ... All of these dogs carry haplotypes that fall under the mDNA a2 sub-haplogroup and are therefore descendants of a dog/Chinese ...
Haplogroup K1a1b1a (mtDNA)
"mtDNA Haplogroup K: K1a1b1a Subclade Haplotypes" (JPG). mtDNA Haplogroup K Project. Websites PhyloTree.Org [1] The Genographic ... of all Ashkenazi mtDNA haplotypes. Approximately 19% of Ashkenazi Jews with ancestry from Poland are in mtDNA haplogroup ...
Linkage disequilibrium
and the estimated frequency of haplotype xy is e. [. h. f. x. y. ]. =. D. N. ⋅. B. N. .. {\displaystyle e[hf_{xy}]={\sqrt {{\ ... of the haplotypes in the offspring have not recombined, and are thus copies of a random haplotype in their parents. A fraction ... estimated frequency of haplotype i. j. =. g. f. i. g. f. j. =. 0.0215.. {\displaystyle hf_{ij}={\text{estimated frequency of ... the frequency of the haplotype A. 1. B. 1. {\displaystyle A_{1}B_{1}}. , becomes ...
MHC Haplotype Project
... The MHC Haplotype Project was conducted between 2000 and 2006 at the Sanger ... MHC Haplotype Project Data. The data from the MHC Haplotype Project are available in .txt file format file for viewing in the ... Haplotype HLA-A HLA-B HLA-C HLA-DRB1 HLA-DQB1 HLA-DPB1 Links:. Vega UCSC. GRC ... The data are colour-coded by haplotype and will initially be displayed showing 1Mb in the centre of the MHC. You are then free ...
Haplotype - Wikipedia
... haplotype estimation and haplotype tagging (Homepage). HelixTree - Haplotype analysis software - Haplotype Trend Regression ( ... Haplotype diversity is a measure of the uniqueness of a particular haplotype in a given population. The haplotype diversity (H ... Given the genotypes for a number of individuals, the haplotypes can be inferred by haplotype resolution or haplotype phasing ... haplotype frequency of each haplotype in the sample and N {\displaystyle N} is the sample size. Haplotype diversity is given ...
Haplotype block - Wikipedia
... that explain a majority of the common haplotypes in the sequence (or a lower-than-usual number of unique haplotypes). In 2001, ... and which contain only a small number of distinct haplotypes. According to the haplotype-block model, such blocks should show ... In genetics, a haplotype block is a region of an organisms genome in which there is little evidence of a history of genetic ... The boundaries of haplotype blocks cannot be directly observed; they must instead be inferred indirectly through the use of ...
Haplotype | Definition of Haplotype at Dictionary.com
By comparing haplotypes of a mother and father with those of a fetus, scientists can study how new genetic changes arise. See ... Haplotype definition, a combination of closely linked DNA sequences on one chromosome that are often inherited together: ... a combination of closely linked DNA sequences on one chromosome that are often inherited together: By comparing haplotypes of a ...
CiteSeerX - Pure Parsimony Xor Haplotyping
In this paper we propose a formulation based on a well-known model used in haplotype inference: pure parsimony. We exhibit ... The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies [2]. The xor- ... The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies [2]. The xor- ... In this paper we propose a formulation based on a well-known model used in haplotype inference: pure parsimony. We exhibit ...
Alt Haplotypes Track Settings
Reference Assembly Alternate Haplotype Sequence Alignments (. All Mapping and Sequencing tracks). Display mode: hide. dense. ... Only one haplotype can be included in a reference assembly chromosome sequence. Instead of providing a separate complete ... Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. ... This track shows alignments of alternate locus (also known as "alternate haplotype") reference sequences to main chromosome ...
COX-2 gene promoter haplotypes and prostate cancer risk. - PubMed - NCBI
Haplotype GGCC conferred increased risk in the African American and Nigerian populations. Conversely, haplotype AGGG exhibited ... COX-2 gene promoter haplotypes and prostate cancer risk.. Panguluri RC1, Long LO, Chen W, Wang S, Coulibaly A, Ukoli F, Jackson ... Haplotype analyses revealed modest effects on susceptibility to prostate cancer across populations. ...
Haplotype - Wikipedia
is the (relative) haplotype frequency of each haplotype in the sample and N. {\displaystyle N}. is the sample size. Haplotype ... Haplotype diversity is a measure of the uniqueness of a particular haplotype in a given population. The haplotype diversity (H ... Given the genotypes for a number of individuals, the haplotypes can be inferred by haplotype resolution or haplotype phasing ... HelixTree - Haplotype analysis software - Haplotype Trend Regression (HTR), haplotypic association tests, and haplotype ...
Haplotype - Wikipedia
is the (relative) haplotype frequency of each haplotype in the sample and N. {\displaystyle N}. is the sample size. Haplotype ... BiologyPages/H/Haplotypes.html Kimballs Biology Pages (Creative Commons Attribution 3.0) *^ "haplotype / haplotypes , Learn ... Haplotype diversity is a measure of the uniqueness of a particular haplotype in a given population. The haplotype diversity (H ... Given the genotypes for a number of individuals, the haplotypes can be inferred by haplotype resolution or haplotype phasing ...
Direct determination of haplotypes from single DNA molecules. - PubMed - NCBI
The two full haplotypes of the six SNPs comprising fragment 1 are T-G-T-C-T-T and G-C-C-G-G-C for SNPs 5,6,7,8,9,10. Haplotypes ... Six SNPs in fragment 1 were haplotyped in two groups. Two predominant haplotypes were found for the first (SNPs 5,7,9,10) and ... Direct determination of haplotypes from single DNA molecules.. Xiao M1, Wan E, Chu C, Hsueh WC, Cao Y, Kwok PY. ... Determining the long-range haplotypes in a diploid individual is a major technical challenge. Here we report a method of ...
A haplotype map of the human genome. - PubMed - NCBI
A haplotype map of the human genome.. International HapMap Consortium.. Abstract. Inherited genetic variation has a critical ... Genealogical relationships among haplotypes and r2 values in a region without obligate recombination events ... Recombination rates in cM Mb−1 (blue). Non-redundant haplotypes with frequency of at least 5% in the combined sample (bars) and ... The left part of the plot shows the seven different haplotypes observed over this region (alleles are indicated only at SNPs), ...
Accuracy of Genomic Selection Using Different Methods to Define Haplotypes | Genetics
Number of haplotypes per locus for model HAP_IBD, and average total number of haplotypes for all four models, averaged across ... The number of haplotype effects that needs to be estimated can be reduced by including more markers per haplotype and perhaps ... The estimated haplotype variance at each locus was calculated as the heterozygosity of the haplotypes at that locus multiplied ... In the SNP1 model, a haplotype was defined as a marker allele on a single locus, yielding two random haplotype effects per ...
Patent US20060008799 - Rapid haplotyping by single molecule detection - Google Patents
The present invention includes a method for rapid haplotyping a DNA or RNA segment. Two or more target sites on a segment of ... presence or absence of each luminescent hybridization probe on each DNA or RNA segment is detected to determine the haplotype ... a) Targets of haplotyping are all sorts of DNA and RNA variations that are necessary to define a haplotype. They include any ... The haplotype deduced from a genotype is typically done in bulk as follows (inferred haplotypes). The region of interest is PCR ...
Conditional Probability Methods for Haplotyping in Pedigrees | Genetics
Conditional Probability Methods for Haplotyping in Pedigrees Message Subject (Your Name) has forwarded a page to you from ... Conditional Probability Methods for Haplotyping in Pedigrees. Guimin Gao, Ina Hoeschele, Peter Sorensen and Fengxing Du ... Conditional Probability Methods for Haplotyping in Pedigrees. Guimin Gao, Ina Hoeschele, Peter Sorensen and Fengxing Du ... Conditional Probability Methods for Haplotyping in Pedigrees. Guimin Gao, Ina Hoeschele, Peter Sorensen and Fengxing Du ...
HaploRec: Efficient and accurate large-scale reconstruction of haplotypes
... HaploRec [1,2] is a statistical haplotype ... A Markov Chain Approach to Reconstruction of Long Haplotypes. Proceedings of the 9th Pacific Symposium on Biocomputing (PSB04 ... HaploRec: Efficient and accurate large-scale reconstruction of haplotypes. BMC Bioinformatics 7:542, 2006. ... 2.0 (June 2005) This version introduced an EM-based algorithm and a segmentation-based haplotype probability model, and ...
Efficient inference of haplotypes from genotypes on a pedigree
We prove that the problem of finding a minimum-recombinant haplotype configuration (MRHC) is in general NP-hard. This is the ... We study haplotype reconstruction under the Mendelian law of inheritance and the minimum recombination principle on pedigree ... Efficient inference of haplotypes from genotypes on a pedigree J Bioinform Comput Biol. 2003 Apr;1(1):41-69. doi: 10.1142/ ... We study haplotype reconstruction under the Mendelian law of inheritance and the minimum recombination principle on pedigree ...
Unexpected complexity in the haplotypes of commonly used inbred strains of laboratory mice | PNAS
... then a few markers will be sufficient to identify common haplotypes. The approach is identical to the exploitation of haplotype ... Haplotype structure of 1,450 diallelic variants with SDP frequency ,1% between eight inbred strains across a 4.8-Mb region of ... We show that the definition of haplotype blocks is not robust and that methods for QTL mapping may fail if they assume a simple ... Unexpected complexity in the haplotypes of commonly used inbred strains of laboratory mice. B. Yalcin, J. Fullerton, S. Miller ...
High Performance Computing for Haplotyping: Models and Platforms | SpringerLink
In Haplotype Assembly (HA), all heterozygous Single Nucleotide Polymorphisms (SNPs)... ... The reconstruction of the haplotype pair for each chromosome is a hot topic in Bioinformatics and Genome Analysis. ... The reconstruction of the haplotype pair for each chromosome is a hot topic in Bioinformatics and Genome Analysis. In Haplotype ... Gabriel, S.B., et al.: The structure of haplotype blocks in the human genome. Science 296(5576), 2225-2229 (2002)CrossRefGoogle ...
NIOSHTIC-2 Publications Search - 20024990 - Logistic regression model for analyzing extended haplotype data.
... has been used to determine absolute extended haplotypes in diploid genomes. We describe statistical analyses for comparing ... there has been increased interest in evaluating extended haplotypes in p53 as risk factors for cancer. An allele-specific ... The method can also be applied to any polymorphic system, whether multiple alleles at a single locus or multiple haplotypes ... Recently, there has been increased interest in evaluating extended haplotypes in p53 as risk factors for cancer. An allele- ...
Haplotype - SNPedia
Haplotype: A specific combination of SNPs all occuring together on the same chromosome (i.e. all occuring on the chromosome ... Haplotypes are important for example because many of the SNPs found by genome-wide association studies arent the true cause ... Because haplotypes are highly likely to be preserved in populations, there are several algorithms for attempting to conduct ... Next Gen Sequencing can thus provide not only perfectly phased genome, but also a haplotype map which can be used to impute ...
Creating a Single Haplotype Human Genome Assembly.
A haplotype map of the human genome
Blocks of Limited Haplotype Diversity
... and with low haplotype diversity, separated from other blocks by steps of low LD with high haplotype diversity ... A haplotype block is a DNA sequence containing polymorphisms in strong linkage disequilibrium (LD) ... and with low haplotype diversity, separated from other blocks by steps of low LD with high haplotype diversity. Haplotype ... Haplotype diversity measured by the effective number of haplotypes is said to be low if smaller than the number of ...
Which ethnic groups carry high risk DR-DQ haplotypes for type 1 diabetes mellitus (DM)?
In African Americans, the DRB1*07:01 - DQA1*03:01 -DQB1*02:01g haplotype is ass... more ... These high-risk haplotypes are found primarily in people of European descent; other ethnic groups are less well studied. ... These high-risk haplotypes are found primarily in people of European descent; other ethnic groups are less well studied. In ... HLA DR-DQ haplotypes and genotypes and type 1 diabetes risk: analysis of the type 1 diabetes genetics consortium families. ...
Protective Effect of the MCP-1 Gene Haplotype against Schizophrenia
... Hana Saoud,1 Oumaima Inoubli,1 Sihem Ben Fredj,2 Mohsen ... Haplotype distribution profile suggests that the observed protection status may be driven more strongly by the MCP-1 -2518G ... Table 3: Haplotype analysis of MCP-1 polymorphisms in patients with schizophrenia and control subjects. ... J. C. Barrett, B. Fry, J. Maller, and M. J. Daly, "Haploview: analysis and visualization of LD and haplotype maps," ...
Transmission of DQ haplotypes to patients with type 1 diabetes. | Diabetes
Transmission of DQ haplotypes to patients with type 1 diabetes.. E Kawasaki, J Noble, H Erlich, C L Mulgrew, P R Fain, G S ... Transmission of DQ haplotypes to patients with type 1 diabetes.. E Kawasaki, J Noble, H Erlich, C L Mulgrew, P R Fain, G S ... Transmission of DQ haplotypes to patients with type 1 diabetes. Message Subject (Your Name) has forwarded a page to you from ...
A Note on Efficient Computation of Haplotypes via Perfect Phylogeny | UMIACS
A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. Title. A Note on Efficient Computation of Haplotypes via ... A Haplotype Map project has been announced by NIH to identify and characterize populations in terms of these haplotypes. ... For the second problem of computing a PPH solution that minimizes the number of distinct haplotypes, we show that the problem ... The problem of inferring haplotype phase from a population of genotypes has received a lot of attention recently. This is ...
A First-Generation Haplotype Map of Maize | Science
A First-Generation Haplotype Map of Maize. By Michael A. Gore, Jer-Ming Chia, Robert J. Elshire, Qi Sun, Elhan S. Ersoz, Bonnie ... A First-Generation Haplotype Map of Maize. By Michael A. Gore, Jer-Ming Chia, Robert J. Elshire, Qi Sun, Elhan S. Ersoz, Bonnie ... S6) (22). However, we also found evidence of longer haplotypes extending for thousands and millions of bases. Association ... among 27 diverse maize inbred lines and discovered that the genome was characterized by highly divergent haplotypes and showed ...
Genaissance, AstraZeneca Align To Apply Haplotypes To Disease | BioWorld
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GenotypeSNPsPopulationsAllelesGeneticGenotypesFrequenciesDistinct haplotypesLociGenesSusceptibilityDifferent haplotypes2001FrequencyWhole genomeRecombinationLocusGeneticsLinkageAlleleMethodsDiversityPolymorphismsAlgorithmAlgorithmsSequencesSequenceMtDNAMarker haplotypeMutationsMarkersInferVariantsAnalysesHapMapAnalysis of genomicsSupporting the hypothesisProbabilityDiseasePairsDRB1DiploidBlocksPhenotypeDataPure parsimonyHypothesisChromosome regionsCommonSubstantiallyGenome-wide asAutosomalHuman GenomicsFetal HemoglobinVariationGenomesExon
Genotype16
- A haplotype (haploid genotype) is a group of alleles in an organism that are inherited together from a single parent. (wikipedia.org)
- The haploid genotype (haplotype) is a genotype that considers the singular chromosomes rather than the pairs of chromosomes. (wikipedia.org)
- An organism's genotype may not define its haplotype uniquely. (wikipedia.org)
- The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies [2]. (psu.edu)
- 2002). Given a meiotic model for the combination of a pair of haplotypes into a genotype during mating, and given a set of observed genotypes in a sample from a human population, it is of great interest to identify the underlying haplotypes (Stephens et al. (psu.edu)
- These data also indicate that the risk associated with specific HLA haplotypes can be influenced by the genotype context and that the trans- complementing heterodimer encoded by DQA1*0501 and DQB1*0302 confers very high risk. (diabetesjournals.org)
- In this study, we investigated whether haplotype (genotype + phase) information would strengthen the genotype-phenotype relationship for PON1. (aacrjournals.org)
- Collectively, the genetic (genotype or haplotype) contribution to PON1 enzymatic activity (measured as phenylacetate hydrolysis) was greater in neonates compared with mothers. (aacrjournals.org)
- Hence genotype (blended) SNP data will be collected, and the desired haplotype (partitioned) data must then be (partially) inferred. (biomedsearch.com)
- Modern genotyping technologies do not measure haplotypes directly, but the combined sum (or genotype) of alleles at each site. (plos.org)
- These haplotypes can be used to guide genotype imputation and haplotype estimation. (ashg.org)
- 5%. I will describe our evaluation of strategies for merging haplotypes and variant lists across studies and advances in methods for genotype likelihood-based haplotype estimation that can be applied to 10,000s of samples. (ashg.org)
- The majority of haplotypes will also be deposited in the European Genotype Archive. (ashg.org)
- The method makes use of available offspring genotype information to apportion ambiguous haplotypes for the subjects. (umich.edu)
- For subjects without offspring genotype information, haplotypes are apportioned as in the standard EM algorithm for case-control data. (umich.edu)
- These haplotype probabilities provide the key quantities for developing hidden Markov models for the treatment of missing genotype information. (g3journal.org)
SNPs26
- There are two main ways that the term "haplotype block" is defined: one based on whether a given genomic sequence displays higher linkage disequilibrium than a predetermined threshold, and one based on whether the sequence consists of a minimum number of single nucleotide polymorphisms (SNPs) that explain a majority of the common haplotypes in the sequence (or a lower-than-usual number of unique haplotypes). (wikipedia.org)
- proposed the following definition of the term: "Suppose we have a number of haplotypes consisting of a set of consecutive SNPs. (wikipedia.org)
- Six SNPs in fragment 1 were haplotyped in two groups. (nih.gov)
- The two full haplotypes of the six SNPs comprising fragment 1 are T-G-T-C-T-T and G-C-C-G-G-C for SNPs 5,6,7,8,9,10. (nih.gov)
- These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. (nih.gov)
- If single-nucleotide polymorphisms (SNPs) are randomly distributed across the genomes of inbred strains, mapping QTL by SDP association with phenotype will require a very dense set of markers, but if the distribution is segmented, then a few markers will be sufficient to identify common haplotypes. (pnas.org)
- In Haplotype Assembly (HA), all heterozygous Single Nucleotide Polymorphisms (SNPs) have to be assigned to exactly one of the two chromosomes. (springer.com)
- Most genotyping experts won't admit it in public, but there is a friendly feud simmering between proponents of SNPs and proponents of haplotypes. (genomeweb.com)
- Haplotypes are just ordered arrays of SNPs, and this is just more information and better information. (genomeweb.com)
- Do you think haplotypes eventually will usurp SNPs as drug-discovery clues? (genomeweb.com)
- When you find them - we found there are there are 3,000 of them - you take these genes, sequence the genomes of 15 individuals to find all of the SNPs in those genes, and define haplotypes. (genomeweb.com)
- The data from this effort will contribute to the development of a map, called the HapMap, of the haplotype patterns in the human genome and of a set of SNPs that are informative about these patterns and the associations among the SNPs. (nih.gov)
- This means that although a region may contain many SNPs, it can be characterized by a few SNPs that uniquely identify, or "tag", each of the haplotypes in the region. (nih.gov)
- The goal of the International HapMap Project is to produce a resource that describes the haplotypes in the human genome and the SNPs that tag them. (nih.gov)
- 5%), while the remaining three SNPs were found on multiple haplotypes, suggesting a complex history of recombination. (nature.com)
- Significant associations to a single disease outcome were found for two SNPs and one haplotype in AA. (nature.com)
- In addition, given the important role played by SDF-1 and CXCR4 in HIV-1/AIDS, we looked for the influence of genetic variation in these SNPs and haplotypes on disease in over 3000 subjects enrolled in five USA-based natural history HIV-1/AIDS cohorts. (nature.com)
- I am a little bit confused about the relationship between LD, haplotypes and SNPs. (biology-online.org)
- Generally, SNPs together with other genetic variants (like disease alleles) can be inherited in/as haplotypes, which means they are in LD. (biology-online.org)
- The HapMap project identifies common haplotype blocks and the specific SNPs that uniquely identify them (tag SNPs). (biology-online.org)
- So the idea of the HapMap Project is to identify haplotypes and tag SNPs. (biology-online.org)
- Using tag SNPs, one can find chromosome regions that have different haplotype distributions in two groups of people (one with disease, one control). (biology-online.org)
- Single SNPs and haplotypes were analysed for associations with disease risk, age parameters, mini-mental state examination scores and cerebrospinal fluid biomarkers for AD using logistic or linear regression. (lu.se)
- The strongest association was found for a haplotype consisting of the 8 OPN SNPs rs2728127-rs2853744-rs11730582-rs11439060-rs28357094-rs112661-rs1126772-rs9138 (omnibus p-value = 2.07×10⁻⁸). (uni-muenchen.de)
- This book constitutes the post-proceedings of the DIMACS/RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotype Inference held in Piscataway, NJ, USA, in November 2002. (springer.com)
- The haplotype was further studied using a fusion gene containing multiple ERCC1 SNPs. (bmj.com)
Populations22
- Haplotype analyses revealed modest effects on susceptibility to prostate cancer across populations. (nih.gov)
- Haplotype GGCC conferred increased risk in the African American and Nigerian populations. (nih.gov)
- The SNP1 model considers only two haplotypes at a locus and therefore may be suited for applications in, for instance, double-haploid populations with only two segregating genotypes at each locus ( X u 2003 ). (genetics.org)
- Because haplotypes are highly likely to be preserved in populations, there are several algorithms for attempting to conduct pseudo-phasing on large number of unrelated people. (snpedia.com)
- This can lead to over-estimation of the risk by including odds ratio of different SNP's along same haplotype, or flip-flop phenomenon where the effect of the SNP is opposite in different populations due to population-dependent variation in the haplotype. (snpedia.com)
- 2001). A Haplotype Map project has been announced by NIH to identify and characterize populations in terms of these haplotypes. (umd.edu)
- While an individual human could exhibit any of 2k different patterns of markers on a single chromosome, in real populations only a small subset of such patterns-haplotypes-are actually observed (Gabriel et al. (psu.edu)
- The identification of such haplotypes would have significant implications for the understanding of the migration patterns of ancestral populations of humans. (psu.edu)
- It will be used in large-scale screens of populations to associate specific haplotypes with specific complex genetic-influenced diseases. (psu.edu)
- Rare haplotypes in mtDNA: applications in the analysis of biosocial aspects of past human populations. (blogspot.com)
- A combination of haplotype H and 73G in HVS-II, rare in extant populations (0.5-3%), has been found at a frequency of 20% in the ancient population of Aldaieta. (blogspot.com)
- The major genetic determinants of type 1 diabetes are alleles at the HLA-DRB1 and DQB1 loci, with both susceptible and protective DR-DQ haplotypes present in all human populations. (diabetesjournals.org)
- Most common haplotypes occur in all human populations, although their frequencies may vary among populations. (nih.gov)
- The Jewish populations were characterized by a diverse set of 13 haplotypes that were also present in non-Jewish populations from Africa, Asia, and Europe. (pnas.org)
- Recent developments in statistical methods have permitted the reconstruction of haplotypes and the estimation of haplotype frequencies in unrelated populations based on SNP data. (aacrjournals.org)
- A practical algorithm for optimal inference of haplotypes from diploid populations. (biomedsearch.com)
- Recently, we and others made the unexpected finding that V617F JAK2 is not acquired randomly but instead arises preferentially on a specific constitutional JAK2 haplotype, at least in white populations. (bloodjournal.org)
- A recent study using mitochondrial DNA analysis demonstrated substantial genetic variation among ponderosa pine populations in the western U.S., identifying 10 haplotypes with unique evolutionary lineages that generally correspond spatially with distributions of the Pacific (P. p. var. (usda.gov)
- All G6PD*A- alleles share the RFLP-microsatellite haplotype - - /195, the same haplotype described in nearly all the *A- alleles from sub-Saharan, Mexican Mestizo, and Portuguese populations, consistent with a single and recent origin of the G202A mutation on this *A haplotype. (bioone.org)
- Genetic analysis of human populations worldwide showed that haplotypes with −21M HLA-B rarely encoded the KIR ligands Bw4+HLA-B and C2+HLA-C. Thus, there are two fundamental forms of HLA haplotype: one preferentially supplying CD94/NKG2A ligands and the other preferentially supplying KIR ligands. (ovid.com)
- Among these we found an individual (young adult male) with a mitochondrial DNA haplotype that had previously only been identified in modern Romani populations. (royalsocietypublishing.org)
- D). An HMM for this purpose formally requires the calculation of two-locus diplotype probabilities, although if the populations are formed with a large number of mating pairs, the two haplotypes within an individual are independent, and so it is sufficient to calculate two-locus haplotype probabilities. (g3journal.org)
Alleles17
- The table below lists the eight cell lines used in the project along with their HLA haplotypes and alleles. (ucl.ac.uk)
- It is thought that identifying these statistical associations and a few alleles of a specific haplotype sequence can facilitate identifying all other such polymorphic sites that are nearby on the chromosome. (wikipedia.org)
- The models estimated the effect of (1) each single-marker allele [single-nucleotide polymorphism (SNP)1], (2) haplotypes constructed from two adjacent marker alleles (SNP2), and (3) haplotypes constructed from 2 or 10 markers, including the covariance between haplotypes by combining linkage disequilibrium and linkage analysis (HAP_IBD2 and HAP_IBD10). (genetics.org)
- The underlying assumption of genomic selection is that haplotypes at some loci are in linkage disequilibrium (LD) with QTL alleles that affect the traits that are subject to selection. (genetics.org)
- Different ways of deriving haplotypes of combinations of marker alleles, and the relationship between haplotypes at a locus, have been described. (genetics.org)
- One method (SNP1) is to consider each different marker allele at a single locus to be a different haplotype, considering no relationships between different haplotypes, and thus breeding values are estimated directly for the marker alleles ( X u 2003 ). (genetics.org)
- A third method is to construct haplotypes (HAP_IBD) using two or more surrounding marker alleles and derive identical-by-descent (IBD) probabilities between the different haplotypes at the same locus ( M euwissen and G oddard 2001 ). (genetics.org)
- A disadvantage of the SNP1 model is that no new haplotypes arise as a result of recombination, while such an event actually might change the linkage between the marker and the QTL alleles. (genetics.org)
- The method can also be applied to any polymorphic system, whether multiple alleles at a single locus or multiple haplotypes over several loci. (cdc.gov)
- Subsequently, it was shown that ~50% of Cohanim carry a characteristic suite of alleles at six Y-linked STRs, which defined the Cohen Modal Haplotype (CMH). (springer.com)
- A specific set of such associated SNP alleles is called a haplotype. (nih.gov)
- These findings suggest that the CYP3A4 and CYP3A5 variants, or other alleles on the haplotypes they help distinguish, are associated with prostate cancer risk and aggressiveness. (aacrjournals.org)
- Every individual carries two copies of each chromosome (haplotypes), one from each of their parents, that consist of a long sequence of alleles. (plos.org)
- Genes are inherited together as haplotypes because of LD, i.e. the non random association of alleles at different loci (they form a block of DNA that is inherited together). (biology-online.org)
- Licínio Manco , Laura R. Botigué , M. Letícia Ribeiro , and Augusto Abade "G6PD Deficient Alleles and Haplotype Analysis of Human G6PD Locus in São Tomé e Príncipe (West Africa)," Human Biology 79(6), 679-686, (1 December 2007). (bioone.org)
- T is in linkage disequilibrium (LD) with causative alleles, and that these haplotypes are more frequent in Caucasians with melanoma than in healthy Caucasians or African Americans. (bmj.com)
- Equation (1) is derived by noting that an AA haplotype drawn from generation F s +1 is either an intact AA haplotype at generation F s , transmitted without recombination, or it is a recombinant haplotype bringing two independent A alleles together. (g3journal.org)
Genetic16
- In genetics, a haplotype block is a region of an organism's genome in which there is little evidence of a history of genetic recombination, and which contain only a small number of distinct haplotypes. (wikipedia.org)
- By comparing haplotypes of a mother and father with those of a fetus, scientists can study how new genetic changes arise. (dictionary.com)
- 3 . The method of claim 1 , further including the step of sequentially and repeatedly haplotyping pairs of neighboring genetic makers on DNA segments forming a chromosome. (google.com)
- Haplotypes have also important applications in genetic genealogy and determining identity by descent . (snpedia.com)
- To be useful in genetic analysis, the haplotype should be shorter than a typical block. (els.net)
- Recently, Gusfield introduced the perfect phylogeny haplotyping problem, as an algorithmic implication of the no-recombination in long blocks observation, together with the standard population-genetic assumption of infinite sites. (umd.edu)
- The biological key to that strategy is the surprising fact that genomic DNA can be partitioned into long blocks where genetic recombination has been rare, leading to strikingly fewer distinct haplotypes in the population than previously expected [12, 6, 21, 7]. (psu.edu)
- And I can find 10 or so publications that will find that the haplotype is always better than the single genetic variant. (genomeweb.com)
- These include haplotypes , genetic sequences that we inherit from only one parent , which allows us to solve our problems with tracking genetic traits and ancestry backward through time and geography. (visionlearning.com)
- Thus, haplotype information may help clarify the genetic influence on PON1 activity. (aacrjournals.org)
- Haplotypes of IL-4 receptor and CD14 genetic polymorphisms are markers of susceptibility for diisocyanate asthma. (cdc.gov)
- Since surnames are highly geographically localized, local geographical patterning of Y haplotypes is a potential confounding factor: genetic structure within names could arise as a result of geographical structure within Britain, rather than due to descent. (bl.uk)
- Haplotype estimation is a key first step of many disease and population genetic studies. (plos.org)
- 31,500 sequenced whole genomes, aggregated over 20 studies of predominantly European ancestry, to create a very large reference panel of human haplotypes where ~50M genetic variants are observed 5 or more times. (ashg.org)
- This package has a function that collapses the haplotypes (unique DNA sequences) in a DNA alignment, something which is extremely useful in various analyses and in the calculation of genetic diversity. (r-bloggers.com)
- Our predictive climate niche models may inform strategies for further genetic research (e.g., sampling design) and conservation that promotes haplotype compatibility with projected changes in future climate. (usda.gov)
Genotypes7
- Given the genotypes for a number of individuals, the haplotypes can be inferred by haplotype resolution or haplotype phasing techniques. (wikipedia.org)
- The problem of inferring haplotype phase from a population of genotypes has received a lot of attention recently. (umd.edu)
- The aim of this study is to estimate the risk conferred by specific DR-DQ haplotypes and genotypes. (diabetesjournals.org)
- Statistical methods are needed to infer (or phase) the haplotypes from the observed genotypes. (plos.org)
- The estimation of haplotypes from SNP genotypes, commonly referred to as 'phasing', is a well studied problem in the literature. (plos.org)
- But often we will have offspring for at least some of the spouse pairs, and offspring genotypes provide additional information about the haplotypes of the parents. (umich.edu)
- For case-control data with some subjects forming spouse pairs and offspring genotypes available for some spouse pairs or individuals, we propose a unified, likelihood-based method of haplotype inference. (umich.edu)
Frequencies3
- Six or five haplotypes were present at frequencies greater than 5% in AA or EA, respectively. (nature.com)
- B 39:1-38) for case-control data can be used to estimate haplotype frequencies. (umich.edu)
- Allele frequencies, gene diversities and haplotype frequencies were analyzed. (scirp.org)
Distinct haplotypes4
- Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. (ucsc.edu)
- Instead of providing a separate complete chromosome sequence for each haplotype, which could cause confusion with divergent chromosome coordinates and ambiguity about which sequence is the official reference, the Genome Reference Consortium (GRC) adds alternate locus sequences, ranging from tens of thousands of bases up to low millions of bases in size, to represent the distinct haplotypes. (ucsc.edu)
- Second, if there are multiple solutions, can we find one that is most parsimonious in terms of the number of distinct haplotypes.We give reductions that suggests that the answer to both questions is "no. (umd.edu)
- For the second problem of computing a PPH solution that minimizes the number of distinct haplotypes, we show that the problem is NP-hard using a reduction from Vertex Cover (Garey and Johnson, 1979). (umd.edu)
Loci6
- These GRC haplotype contigs, called 'alternate loci', are constructed so that they begin with additional anchor sequence derived from the reference. (ucl.ac.uk)
- For a given individual, there are nine possible configurations (haplotypes) at these two loci (shown in the Punnett square below). (wikipedia.org)
- For individuals heterozygous at both loci, the gametic phase is ambiguous - in these cases, you don't know which haplotype you have, e.g. (wikipedia.org)
- We describe statistical analyses for comparing cases and controls, or comparing different ethnic groups with respect to haplotypes composed of several biallelic loci, especially in the presence of other covariates. (cdc.gov)
- However, allelic variation at these loci cannot account fully for the pattern of HLA haplotype sharing among affected sibpairs ( 8 ). (diabetesjournals.org)
- Expression quantitative trait loci (eQTLs) were investigated for variants tagging six SLE-risk or -protective haplotypes: DRB1*03:01 (rs2187668), DRB1*15:01 (rs3135391), DPB1 (rs3117213, rs2071351, rs2071349), and MSH5 (rs409558). (bl.uk)
Genes3
- 2001) Haplotype tagging for the identification of common disease genes. (els.net)
- 2001) Haplotype variation and linkage disequilibrium in 313 human genes. (els.net)
- However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. (wur.nl)
Susceptibility6
- The comparison of closely related DR-DQ haplotype pairs with different type 1 diabetes risks allowed identification of specific amino acid positions critical in determining disease susceptibility. (diabetesjournals.org)
- Instead, multiple polymorphisms defined a set of four common haplotypes (of which two were associated with disease susceptibility and two seemed to be protective) and multiple rare haplotypes (associated with increased susceptibility in aggregate). (nature.com)
- Although the functional significance of these findings is uncertain, these haplotypes could be susceptibility markers for DA and may be useful aids in the diagnosis of DA. (cdc.gov)
- The role of osteopontin (OPN/SPP1) haplotypes in the susceptibility to Crohn's disease. (uni-muenchen.de)
- However, several OPN haplotypes showed significant associations with CD susceptibility. (uni-muenchen.de)
- Our study identified OPN haplotypes as modifiers of CD susceptibility, while the combined effects of certain OPN variants may modulate IL-22 secretion. (uni-muenchen.de)
Different haplotypes3
- Therefore, given a set of possible haplotype resolutions, these methods choose those that use fewer different haplotypes overall. (wikipedia.org)
- The benefit from the HAP_IBD approach is that the common background of haplotypes, and thus the probability that different haplotypes are associated with the same QTL allele, is modeled more accurately. (genetics.org)
- Patients with different haplotypes are assumed to be unrelated and thus to carry independent mutations. (lu.se)
20011
- Daly MJ, Rioux JD, Schaffner SF, Hudson TJ and Lander ES (2001) High‐resolution haplotype structure in the human genome. (els.net)
Frequency11
- The association analysis was performed by comparing the frequency of DR-DQ haplotypes among the chromosomes transmitted to an affected child with the frequency of chromosomes not transmitted to any affected child. (diabetesjournals.org)
- There were seven haplotypes with a frequency of 5% or higher in at least one ethnic group of the study population. (aacrjournals.org)
- OBJECTIVE: To analyze the frequency of the haplotypes of β-globin gene cluster in randomly selected patients with sickle cell disease (SCD), attended in the Children's Hospital of Panama. (biomedsearch.com)
- The frequency of the IC haplotype (shared between I75V and C159T) was 0.44 in DA + workers vs. 023 among DA- subjects (p=0.04). (cdc.gov)
- The QC haplotype frequency (Q576R, C159T) of 0.667 in the DA + group was more frequent (0.425) than in the DA- groups (p=0.03). (cdc.gov)
- Furthermore, the frequency of IQC haplotype (l75V, Q576R, C159T) was 0.44 in DA + workers vs. 0.217 in the DA - group (p=0.04). (cdc.gov)
- Our method enables efficient haplotype frequency estimation using an EM algorithm and supports probabilistic haplotype reconstruction with the probability calculated based on the whole sample. (umich.edu)
- haplotype_pattern_id Frequency OBJECT METHODS See Below for more detailed summaries. (ubuntu.com)
- Generate reliable Y-STR haplotype frequency estimates for Y-STR haplotypes to be used in the quantitative assessment of matches in forensic and kinship casework. (yhrd.org)
- Let p s denote the frequency of the AA haplotype at generation F s . (g3journal.org)
- 2) The frequency of recombinant haplotypes at generation F s is 1 − 2 p s . (g3journal.org)
Whole genome4
- Microfluidic whole genome haplotyping is a technique for the physical separation of individual chromosomes from a metaphase cell followed by direct resolution of the haplotype for each allele. (wikipedia.org)
- Genomic selection uses total breeding values for juvenile animals, predicted from a large number of estimated marker haplotype effects across the whole genome. (genetics.org)
- Browning, S.R., Browning, B.L.: Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. (springer.com)
- The goal of the Haplotype Reference Consortium is to combine haplotype information from ongoing whole genome sequencing studies to create a large imputation resource. (ashg.org)
Recombination5
- According to the haplotype-block model, such blocks should show high levels of linkage disequilibrium and be separated from one another by numerous recombination events. (wikipedia.org)
- We study haplotype reconstruction under the Mendelian law of inheritance and the minimum recombination principle on pedigree data. (nih.gov)
- Verhoeven KJ and Simonsen KL (2005) Genomic haplotype blocks may not accurately reflect spatial variation in historic recombination intensity. (els.net)
- We identified and genotyped several million sequence polymorphisms among 27 diverse maize inbred lines and discovered that the genome was characterized by highly divergent haplotypes and showed 10- to 30-fold variation in recombination rates. (sciencemag.org)
- This recurrence relation is derived in a similar way to that for the autosome, noting that the male haplotype was drawn from his mother, with a chance for recombination, and a random female haplotype is equally likely to have been drawn from her father, without recombination, or from her mother, with the potential for recombination. (g3journal.org)
Locus9
- This track shows alignments of alternate locus (also known as "alternate haplotype") reference sequences to main chromosome sequences in the reference genome assembly. (ucsc.edu)
- Despite these findings, SP remains a explored emerging lineages of dhps mutant haplotypes in Malawi,theDemocraticRepublicoftheCongo,andTanza- major tool for malaria control when administered as a partner niabyusinganalysesofgeneticmicrosatellitesflankingthe drug with artemisinins and as intermittent preventive therapy dhps locus. (cdc.gov)
- G6PD locus haplotype diversity was also investigated using six intragenic RFLPs ( Fok I, Pvu II, Bsp HI, Pst I, Bcl I, Nla III) and a (CTT) n microsatellite 18.61 kb within the G6PD locus. (bioone.org)
- Using mitochondrial DNA isolated from their cheek cells or hair, students perform PCR and a restriction enzyme digest to determine their haplotypes with respect to a locus in the mitochondrial genome. (carolina.com)
- The aHt haplotype has found a higher discriminatory potential than minHt haplotype with a better Pd combined value (0.9999936 vs 0.9999836) and has higher average gene diversity per locus (0.7834 vs 0.7518) in Turkish population. (scirp.org)
- In this article, I derive the two-locus haplotype probabilities on the autosome and X chromosome with these designs. (g3journal.org)
- Darvasi and Soller (1995) derived the two-locus haplotype probabilities for the autosome in AIL. (g3journal.org)
- In this article, I derive the two-locus haplotype probabilities for the autosome and X-chromosome in AIL, HS, and the DO. (g3journal.org)
- Let us first revisit the two-locus autosomal haplotype probabilities in AIL, as they serve as a simple example of the technique used in these calculations (see also Bulmer 1980 , Ch. 3). (g3journal.org)
Genetics2
Linkage4
- The advantage of the SNP1 approach is that determining the linkage phase of the haplotypes is not required and the markers do not need to be mapped. (genetics.org)
- The approach is identical to the exploitation of haplotype blocks (regions of complete or almost complete linkage disequilibrium) in the human genome for association mapping ( 9 ) but requires a different analysis to take advantage of the small number of founder animals from which laboratory strains are descended. (pnas.org)
- A haplotype block is a DNA sequence containing polymorphisms in strong linkage disequilibrium (LD) and with low haplotype diversity, separated from other blocks by steps of low LD with high haplotype diversity. (els.net)
- Currently, the most accurate methods use hidden Markov models (HMMs) to model local haplotype sharing between individuals [1] , [2] , and take advantage of linkage disequilibrium (LD). (plos.org)
Allele3
- An allele-specific polymerase chain reaction (PCR) method, confirmed by restriction analysis, has been used to determine absolute extended haplotypes in diploid genomes. (cdc.gov)
- 7 - 9 This haplotype, which we refer to as 46/1 7 but others have called GGCC, 8 is found in approximately 50% of normal persons and thus is a common, very low penetrance predisposition allele of the type that is typically detected by genome-wide association studies. (bloodjournal.org)
- A relative change in observed phenotypic variation percentage was obtained per marker allele and across marker haplotype combinations when compared to the PHS susceptible cultivar, Tugela-DN. (frontiersin.org)
Methods5
- These methods work by applying the observation that certain haplotypes are common in certain genomic regions. (wikipedia.org)
- We show that the definition of haplotype blocks is not robust and that methods for QTL mapping may fail if they assume a simple block-like structure. (pnas.org)
- A Haplotype Reference Panel of over 31,000 individuals and Next Generation Imputation Methods. (ashg.org)
- Existing methods may either ignore the offspring information, or reconstruct haplotypes for the subjects using offspring information and discard data from those whose haplotypes cannot be reconstructed with high confidence. (umich.edu)
- All relevant current issues in computational methods for SNP and haplotype analysis and their applications to disease associations are addressed. (springer.com)
Diversity6
- Haplotype diversity measured by the effective number of haplotypes is said to be low if smaller than the number of polymorphisms defining the haplotype. (els.net)
- Morton, Newton E(Dec 2007) Blocks of Limited Haplotype Diversity. (els.net)
- Correlations between surname rank and degree of diversity exist: the more common the surname, the greater the diversity of Y-chromosomal haplotypes associated with the name. (bl.uk)
- M. arenaria isolates did not group as a single haplotype, consistent with other reports of diversity within this species. (apsnet.org)
- A team from the Plant Pathology department at the US University has developed the extensive wheat diversity map - a haplotype map - of 62 varieties from across the world. (bakeryandsnacks.com)
- We suggest that an alternative haplotype designated as aHt maybe alternative to minHt in respect of its Y-STR content with the highest gene diversity value. (scirp.org)
Polymorphisms3
- For single nucleotide polymorphisms 'variation' consists of two letters, firstly, the base in the reference sequence, and secondly, the base in the other haplotype. (ucl.ac.uk)
- We demonstrate the utility of this technology by accurately determining the haplotypes consisting of up to 16 single-nucleotide polymorphisms in genomic regions up to 50 kilobases. (nih.gov)
- In order to determine the minimum number of independent repeats of each mutation we have used PCR to examine the five factor IX polymorphisms forming the most informative combinations and we have characterised thc haplotype of each patient. (lu.se)
Algorithm8
- HaploRec [1,2] is a statistical haplotype reconstruction algorithm targeted for large-scale disease association studies. (helsinki.fi)
- 2.0 (June 2005) This version introduced an EM-based algorithm and a segmentation-based haplotype probability model, and featured several computational improvements, allowing the use of larger data sets. (helsinki.fi)
- A polynomial-time exact algorithm for haplotype reconstruction without recombinants is also presented. (nih.gov)
- Bansal, V., Bafna, V.: HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. (springer.com)
- Results: To improve the accuracy of population assignment, we present an algorithm, implemented in the HaploPOP software, that combines markers into haplotypes, without requiring independence. (diva-portal.org)
- The algorithm is based on the Gain of Informativeness for Assignment that provides a measure to decide if a pair of markers should be combined into haplotypes, or not, in order to improve assignment. (diva-portal.org)
- Because complete exploration of all possible solutions for constructing haplotypes is computationally prohibitive, our approach uses a greedy algorithm based on windows of fixed sizes. (diva-portal.org)
- The maximum likelihood-based expectation maximization algorithm and the Bayesian-based algorithm have been the most widely used approaches for haplotype inference. (aacrjournals.org)
Algorithms1
- However, some evidence suggests that different algorithms for identifying haplotype blocks give very different results when used on the same data, though another study suggests that their results are generally consistent. (wikipedia.org)
Sequences3
- It provides the genomic sequences and gene annotation of 8 different HLA-homozygous typing haplotypes (listed below), their resulting variations (see Data below) and ancestral relationships. (ucl.ac.uk)
- For the other seven haplotype sequences links are given to GRC entries (numbers with GL prefixes). (ucl.ac.uk)
- The attribute function above tells you which sequences in x make up which haplotypes in h but it's a bit tedious, particularly when dealing with large data sets. (r-bloggers.com)
Sequence5
- Only one haplotype can be included in a reference assembly chromosome sequence. (ucsc.edu)
- In order to discriminate between repeat copy and allelic copies, the sequence from a single haplotype across these regions is necessary. (ashg.org)
- No difference in sequence, splicing, or expression of JAK2 was found on 46/1 compared with other haplotypes, suggesting that any functional difference of JAK2 on 46/1, if it exists, must be relatively subtle. (bloodjournal.org)
- and it has not been found in any other human population sampled so far (out of a total of more than 10 000 mtDNA haplotypes for this sequence held in the GenBank sequence repository), except the Castle Mall individual reported on here. (royalsocietypublishing.org)
- Templeton, A.R., Crandall, K.A. and Sing, C.F. (1992) A Cladistic Analysis of Phenotypic Associations with Haplotypes Inferred from Restriction Endonuclease Mapping and DNA Sequence Data. (scirp.org)
MtDNA1
- Although polyoma virus middle T-driven tumors showed altered primary and metastatic profiles in previous studies, depending upon nuclear and mtDNA haplotype, the magnitude and direction of changes were not the same in the HER2-driven mammary carcinomas. (aacrjournals.org)
Marker haplotype1
- In this study, the SSR marker haplotype combination of chromosomes 3A and 4A of former and current South African cultivars were compared with the aim to select for improved PHS tolerance levels in future cultivars. (frontiersin.org)
Mutations5
- The term 'haplogroup' refers to the SNP/unique-event polymorphism (UEP) mutations that represent the clade to which a collection of particular human haplotypes belong. (wikipedia.org)
- Haplotype information is relevant to gene regulation, epigenetics, genome-wide association studies, evolutionary and population studies, and the study of mutations. (inria.fr)
- Analysis of further MPL -positive, V617F-negative cases confirmed an excess of 46/1 (n = 176, P = .002), but no association between MPL mutations and MPL haplotype was seen. (bloodjournal.org)
- All but one of thc 13 mutations occur in at least 2 haplotypes thus. (lu.se)
- All but one of thc 13 mutations occur in at least 2 haplotypes thus pinpointing 12 mutational hotspots and mutations that can be clearly considered detrimental. (lu.se)
Markers3
- And those haplotypes will be used as markers to test large cardiovascular cohorts. (genomeweb.com)
- Haplotypes constructed from Y-chromosome markers were used to trace the paternal origins of the Jewish Diaspora. (pnas.org)
- Eight SSR markers targeted from the well-characterized 3A and 4A QTL regions associated with PHS tolerance, were used to conduct targeted haplotype analysis. (frontiersin.org)
Infer2
- We then apply a novel HMM method (duoHMM) to combine the SHAPEIT2 haplotypes with any family information to infer the inheritance pattern of each meiosis at all sites across each chromosome. (plos.org)
- We infer that VDR haplotypes might influence the risk of HIV-1 acquisition. (ebscohost.com)
Variants2
- Our full resource is available to the community through imputation servers that enable scientists to impute missing variants in any study and respect the privacy of subjects contributing to the studies that constitute the Haplotype Reference Consortium. (ashg.org)
- Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds.We propose that the Asian variants are still present because they affect phenotypes thatwere important for ancient traditional, as well as recent, commercial pig breeding. (wur.nl)
Analyses3
- Haplotype estimation in such cohorts is a central step in many downstream analyses. (plos.org)
- Haplotype analyses did not add significantly to the associations found in the single SNP analyses. (lu.se)
- Initial analyses show haplotype data appear to be predictive of PHS tolerance status and germplasm can now be selected to improve PHS tolerance. (frontiersin.org)
HapMap1
- The National Institutes of Health funded the HapMap project to catalog haplotype blocks throughout the human genome. (wikipedia.org)
Analysis of genomics1
- Background: Haplotype phasing is an important problem in the analysis of genomics information. (inria.fr)
Supporting the hypothesis1
- Three haplotypes of F. japonica (including the widespread haplotype) and one F. sachalinensis matched previously identified Japanese haplotypes, supporting the hypothesis of multiple introductions in the US. (springer.com)
Probability1
- However, it is possible to estimate the probability of a particular haplotype when phase is ambiguous using a sample of individuals. (wikipedia.org)
Disease9
- Tests based simply on cross-tabulating all possible haplotypes by disease state cannot be extended to account for other variables measured on the individual. (cdc.gov)
- In a case-control study, the model can be constructed so that each coefficient gives the log odds ratio for disease for an individual with a single copy of the suspect haplotype and another copy of the most common haplotype, relative to an individual with two copies of the most common haplotype. (cdc.gov)
- He is working with researchers in Great Britain to uncover haplotypes implicated in cardiovascular disease, and has also begun looking into ways in which gene-expression data and proteomics tools may nurture his project. (genomeweb.com)
- We describe likelihood ratio and permutation tests to test for disease-haplotype association, and describe three test statistics that are potentially useful for detecting such an association. (umich.edu)
- This project investigates the effect of (i) SLE-associated MHC haplotypes, and (ii) IFN-α stimulation on gene regulation in ex vivo B cells, in order to further our understanding of how these factors contribute to disease risk. (bl.uk)
- These results suggest a regulatory role for disease-associated MHC haplotypes, and implicate BTN3A2 as a novel candidate gene on the DRB1*03:01 haplotype. (bl.uk)
- STRASBURG, PA- A natural history study has provided the first comprehensive clinical description of spinal muscular atrophy (SMA) within the Amish and Mennonite communities and correlates ancestral chromosome 5 haplotypes and SMN2 copy number with disease severity. (clinicforspecialchildren.org)
- 13 These data not only reflect the severity of the disease but also the effect of haplotypes in modulating the SCA phenotype. (scielo.br)
- The Bantu haplotype has been associated with higher disease severity and high incidence of organ, damage while the Benin haplotype is associated with an intermediate clinical course. (scielo.br)
Pairs2
- Then, to ask if a signal of haplotype sharing exists within surnames, 150 pairs of men were recruited, each sharing a British surname, and Y-haplotype sharing assessed within each pair. (bl.uk)
- methodologies for easy analysis of long stretches of DNA (10000s of base pairs) are now needed for haplotype identification. (soton.ac.uk)
DRB13
- In African Americans, the DRB1*07:01 - DQA1*03:01 -DQB1*02:01g haplotype is associated with increased risk (OR 3.96), whereas the DRB1*07:01-DQA1*02:01 - DQB1*02:01g haplotype appears to be protective (OR 0.34). (medscape.com)
- The most susceptible haplotypes are the DRB1*0301-DQA1*0501-DQB1*0201 (odds ratio [OR] 3.64) and the DRB1*0405-DQA1*0301-DQB1*0302, DRB1*0401-DQA1*0301-DQB*0302, and DRB1*0402-DQA1*0301-DQB1*0302 haplotypes (ORs 11.37, 8.39, and 3.63), followed by the DRB1*0404-DQA1*0301-DQB1*0302 (OR 1.59) and the DRB1*0801-DQB1*0401-DQB1*0402 (OR 1.25) haplotypes. (diabetesjournals.org)
- A novel trans-eQTL was identified for DRB1*03:01 haplotypes in the exon array data set, in both resting and IFN-α-stimulated cells, involving down-regulation of BTN3A2 (P (bl.uk)
Diploid1
- Determining the long-range haplotypes in a diploid individual is a major technical challenge. (nih.gov)
Blocks2
- Haplotype blocks may be as short as 2 kb or more than 150 kb, depending both on block definition and the spacing of LD cold spots, which tend to be shorter than blocks. (els.net)
- At the next RECOMB, I hope someone has a data compression method [for SNP data] that blows haplotype blocks out of the water," said population geneticist Andrew Clark during his keynote address. (genomeweb.com)
Phenotype2
- The IC, QC and IQC haplotypes are significantly associated with the DA phenotype. (cdc.gov)
- Ex vivo PK136 (anti-NK1.1) stimulation assays indicated that licensing may not be a binary phenomenon as some Ly49A-MHC class I haplotype combinations produced an intermediate licensing phenotype. (jimmunol.org)
Data8
- The data from the MHC Haplotype Project are available in .txt file format file for viewing in the UCSC Genome Browser . (ucl.ac.uk)
- The data are colour-coded by haplotype and will initially be displayed showing 1Mb in the centre of the MHC. (ucl.ac.uk)
- The results show that the program performs very well on both types of data and will be useful for large scale haplotype inference projects. (nih.gov)
- Logistic regression model for analyzing extended haplotype data. (cdc.gov)
- Citation Query A new statistical method for haplotype reconstruction from population data. (psu.edu)
- A new statistical method for haplotype reconstruction from population data. (psu.edu)
- The haplotype marker data and phenotypic PHS data were compared across all cultivars and different production regions. (frontiersin.org)
- These haplotype data are the first of its kind for PHS genotyping in South Africa. (frontiersin.org)
Pure parsimony1
- In this paper we propose a formulation based on a well-known model used in haplotype inference: pure parsimony. (psu.edu)
Hypothesis3
- 7 , 8 , 11 First, 46/1 may be inherently more genetically unstable, acquiring V617F at a faster rate than other haplotypes (hypermutability hypothesis). (bloodjournal.org)
- Second, V617F may arise on all haplotypes at equal rates, but 46/1 may carry an additional factor that either gives a selective advantage to the V617F-positive clone or interacts in some way to increase the likelihood of abnormal blood counts (fertile ground hypothesis). (bloodjournal.org)
- Using a novel mouse model, a mitochondrial-nuclear exchange model termed MNX, we tested the hypothesis that inherited mitochondrial haplotypes alter primary tumor latency and metastatic efficiency. (aacrjournals.org)
Chromosome regions1
- Most chromosome regions have only a few common haplotypes. (nih.gov)
Common4
- Clade here refers to a set of haplotypes sharing a common ancestor. (wikipedia.org)
- A haplogroup is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation. (wikipedia.org)
- SNP1 and SNP2 do not make a distinction between haplotypes that are alike-in-state (AIS) due to a common ancestor ( i.e . (genetics.org)
- The most common SELE haplotype in this analysis ([C;G;T;C;G;T], 31.2%) showed a negative association with myocardial infarction (MI) (CAD/MI(+) vs. non-CAD) under the additive (p = 0.001), dominant (p = 0.006) and recessive (p = 0.012) model. (termedia.pl)
Substantially3
- Conclusions: Our results show that constructing haplotypes with HaploPOP can substantially reduce assignment error. (diva-portal.org)
- Haplotype composition varied substantially with respect to ethnicity. (aacrjournals.org)
- Furthermore, the authors noted that the Bantu haplotype substantially influences the levels of this cytokine, elevating its plasma concentration. (scielo.br)
Genome-wide as1
- Haplotypes are important for example because many of the SNP's found by genome-wide association studies aren't the true cause but simply occur on same haplotype and are thus inherited together. (snpedia.com)
Autosomal1
- so, unlike autosomal haplotypes, there is effectively not any randomisation of the Y-chromosome haplotype between generations. (wikipedia.org)
Human Genomics1
- The next high-priority phase of human genomics will involve the development of a full Haplotype Map of the human genome [12]. (psu.edu)
Fetal Hemoglobin1
- 1 , 2 SCA is characterized by a variable clinical course and differences in response to medication, reflecting its complex pathophysiology and suggesting that it can be affected by modulator factors such as the haplotypes of the beta globin chain or fetal hemoglobin (Hb F) levels. (scielo.br)
Variation2
- The haplotype is converted to number , considering the first variation as zero and the alternate value as 1 (see expanded description below). (ubuntu.com)
- Clear favorable haplotypes, contributing 40-60% of the variation for PHS tolerance, were identified for QTL 3A and 4A. (frontiersin.org)
Genomes1
- The working directory of the 1000 Genomes ftp site contains phased haplotypes for 2,123 individuals from the 1000 Genomes Project ( US / Europe ). (blogspot.com)
Exon2
- The 46/1 haplotype was also overrepresented in cases without V617F (n = 347, P = .009), with an excess seen for both MPL exon 10 mutated and V617F, MPL exon 10 nonmutated cases. (bloodjournal.org)
- Identification of NURR1 (Exon 4) and FOXA1 (Exon 3) Haplotypes Associated with mRNA Expression Levels in Peripheral Blood Lymphocytes of Parkinson's Patients in Small Indian Population. (thefreelibrary.com)