Chromosome haplotype. Medical search. Frequent questions

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)
The International HapMap Consortium is a collaboration among researchers in six countries: Japan, the United Kingdom, Canada, China, Nigeria, and the U.S. An earlier RFA ( https://grants.nih.gov/grants/guide/rfa-files/RFA-HG-02-005.html ) solicited research proposals for genotyping SNPs in the chromosomes that are to be done by U.S. researchers for the Project, which is almost one-third of the genome. (nih.gov)
SNPs, haplotypes, and model selection in a candidate gene region: the SIMPle analysis for multilocus data. (nih.gov)
Here, we present a genotype-level analysis to jointly model the SNPs via a SNP interaction model with phase information (SIMPle) to capture the underlying haplotype structure. (nih.gov)
Thus, rather than selecting between genotype- or haplotype-level approaches, the SIMPle method frames the analysis of multilocus data in a model selection paradigm, the aim to determine which SNPs, phase terms, and linear combinations best describe the relation between genetic variation and a trait of interest. (nih.gov)
Four haplotype tagging SNPs were selected that accounted for 83% of the common haplotypic variation in GSTP1 . (nih.gov)
SNPs of the Y-chromosome are always labelled with a letter and a number for identification. (igenea.com)
SNPs (promounced snips)" are found along the chromosome at about 1 every 600-1,000 basepairs. (exploringnature.org)
It is believed that the genome may have as many as 180, 000 haplotype blocks of SNPs. (exploringnature.org)
rs4778241 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. (snpedia.com)
and (iii) molecular analysis of the haemoglobin S mutation, the haplotype in the ß-globin-like genes cluster, the 3.7 kb Î±-thalassaemia gene deletion and 19 selected single-nucleotide polymorphisms (SNPs) associated with fetal haemoglobin (HbF) levels.Results. (bvsalud.org)

By May 2023 about 350.000 Y chromosomes typed for 9-29 STR loci have been directly submitted by worldwide forensic institutions and universities. (wikipedia.org)
Additionally, as the number of loci expands for a haplotype, ambiguity in interpretation increases for determining the underlying genetic components driving a detected association. (nih.gov)
In this study, the haplotype analysis for two loci showed an association between the dwarfing alleles and increased resistance to FHB. (usda.gov)

Hybrids between different species might be expected to suffer deleterious incompatibilities because alleles from orthologous genes from different species may not interact well in hybrids, and if these genes are on the sex chromosomes and are recessive, the heterogametic sex is likely to suffer the most. (nature.com)
The genes that confer actions, are likely to provide important information susceptibility to IDDM are located in the HLA region regarding the causes of IDDM and lead to approaches of chromosome 6. (nih.gov)
Among these "selfish" genes are the t-haplotype. (bigthink.com)
Celiac disease is strongly associated with HLA class II D-region genes in the major histocompatibility complex on chromosome 6. (medscape.com)
15. Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype. (nih.gov)
The site's design allows users to navigate the complex interrelationships among conditions, genes, and chromosomes. (nih.gov)
Two chromosomes overlapped with the major height genes. (usda.gov)
The QTL on chromosomes 4B and 4D overlapped with the major height genes Rht-B1 and Rht-D1, respectively. (usda.gov)
They experience recombination - where pieces of genetic material are swapped from matching chromosomes to form new mixtures of genes. (exploringnature.org)
A) The physical structure of RHD and RHCE genes on the short arm of chromosome 1. (nih.gov)

When scientists study populations of a given ethnic group, they generate one family tree based on the populations' Y-chromosomes and another one based on mtDNA. (visionlearning.com)
There are SNP tests for mtDNA and Y-chromosomes. (igenea.com)

Here we describe a computational strategy to reliably determine complete whole-chromosome haplotypes using a combination of bulk long-range sequencing and Hi-C sequencing. (biomedcentral.com)

Y-chromosome haplotypes are subject to random mutation and the discovery of numerous different haplotypes led scientists to construct the Y-chromosome family tree. (visionlearning.com)
Haplotype analysis was performed to identify the genetic source of the mutation(s). (spandidos-publications.com)
Haplotype analysis suggested the presence of maternal mosaicism for this mutation. (spandidos-publications.com)
identify the haplotype associated with SCD mutation among Bahrainis. (who.int)
In 2001, mutations were discovered in the IKB kinase-complex-associated protein ( IKBKAP ) gene, with a major haplotype mutation located in the donor splice site of intron 20. (medscape.com)

In a Neolithic sample from Derenburg , neither of the two major Y-chromosome haplogroups prevalent in Central-Northern Europe, R1 and I were found. (blogspot.com)

13. Worldwide distribution of the MYH9 kidney disease susceptibility alleles and haplotypes: evidence of historical selection in Africa. (nih.gov)

Theoretically, such transitions can happen on the same pair of sex chromosomes (homologous transition) or involve an autosome, which then becomes a new sex chromosome (heterologous transition). (nature.com)
Haplotype phase represents the collective genetic variation between homologous chromosomes and is an essential feature of non-haploid genomes. (biomedcentral.com)

This study reports a common locus for AIS in the British population, mapping to a refined interval on chromosome 9q31.2-q34.2 and defines a novel AIS locus on chromosome 17q25.3-qtel. (bmj.com)
The haplotype analysis of ihs locus on chromosome 18 using 96 N 2 progeny. (figshare.com)

A Y-chromosome haplogroup contains men who share a common ancestor in their pure paternal ancestral lineage. (igenea.com)

During the hybridisation process, the sex-determining region of the X chromosome from one parental species was translocated to an autosome in the hybrids leading to the evolution of a new sex chromosome. (nature.com)
We reconstruct full parental haplotypes and quantify changes in parental allele-specific expression, genome-wide. (nih.gov)
Trio-binning uses short Illumina reads from the two parental genomes to partition the long reads obtained from the heterozygous offspring into haplotype-specific sets. (usda.gov)
Each haplotype is then assembled independently to reconstruct the two parental genomes. (usda.gov)
The Canu assembly contained 12,416 and 13,021 contigs with an N50 contig length of 768,218bp and 796,316bp for the female and male parental haplotypes, respectively. (usda.gov)

either there was no chromosomal sex determination in the last common ancestor and both systems developed independently, or one lineage retained the ancestral sex chromosomes while in the other lineage a transition to the alternate system occurred. (nature.com)
An ancestral inversion of 900 kb on chromosome 17q21, which includes the microtubule-associated protein tau ( MAPT ) gene, defines two haplotype clades in Caucasians (H1 and H2). (frontiersin.org)
There are two common MAPT extended haplotypes in Caucasians resulting from an ancestral inversion: H1 and H2. (frontiersin.org)
Detailed analysis delineated a prominent ancestral haplotype that accounted for approximately 50% of HD chromosomes and extended to at least 938 kb on about half of these. (healthpartners.com)

Two important objectives are pursued: (1) the generation of reliable frequency estimates for Y-STR haplotypes and Y-SNP haplotypes to be used in the quantitative assessment of matches in forensic and kinship cases and (2) the characterization of male lineages to draw conclusions about the origins and history of human populations. (wikipedia.org)
The population genetic history of a 10.1-kbp noncoding region of the human X chromosome was studied using the males of the HGDP-CEPH Human Genome Diversity Panel (672 individuals from 52 populations). (blogspot.com)
The geographic distribution of patterns of variation was roughly consistent with previous studies, with the major exception that 1 highly divergent haplotype (haplotype X, hX) was observed at low frequency in widely scattered non-African populations and not at all observed in sub-Saharan African populations. (blogspot.com)
Most common haplotypes occur in all human populations, although their frequencies may vary among populations. (nih.gov)
A network analysis showed the extent of distribution of haplotypes of various populations and their relationships. (bl.uk)
10. Comparison of linkage disequilibrium patterns and haplotype structure of eight single nucleotide polymorphisms across the CYP1A2 gene between the Korean, and other populations registered in the International HapMap database. (nih.gov)
17. Interleukin-8 genetic diversity, haplotype structure and production differ in two ethnically distinct South African populations. (nih.gov)
Genetic characterization of populations of the Volga-Ural region according to the variability of the Y-chromosome. (snpedia.com)
Y Chromosome analysis of prehistoric human populations in the West Liao River Valley, Northeast China. (snpedia.com)

Medical genetics is rapidly evolving from its capacity to identify single-gene disorders such as phenylketonuria and cystic fibrosis, and single-chromosome disorders such as Down syndrome, toward understanding of multiple-gene and gene-environment interactions associated with complex conditions such as cardiovascular disease, diabetes, asthma and cancers. (ishrs.org)
As chromosomes are spatially isolated in separate territories in the cell nucleus, Hi-C contacts are predominantly formed within a single chromosome and can reveal cis linkage across the entire chromosome [ 36 ] without single-chromosome isolation. (biomedcentral.com)

The reason for this is simple but has proven difficult to tackle - instead of inheriting one copy of every chromosome from both the father and from the mother (as in humans) potatoes inherit two copies of each chromosome from each parent, making them a species with four copies of each chromosome (tetraploid). (mpg.de)
In humans, the genome consists of 23 pairs of chromosomes (found in the nucleus), plus a small chromosome (found in the cells' mitochondria). (visionlearning.com)
Extended Y chromosome investigation suggests postglacial migrations of modern humans into East Asia via the northern route. (snpedia.com)
C) Resolving the crossed-over chromosome yields the RH gene structure of the extant RHD negative haplotype that is prevalent in humans. (nih.gov)

Background: Past work on asthmatic African American families revealed a strong linkage peak with modest evidence of association on chromosome 11q. (tmu.edu.tw)
Significant linkage was obtained in a total of 10 families: 8 families to the telomeric region of chromosome 9q, and 2 families to the telomeric region of 17q. (bmj.com)
14. The importance of a sub-region on chromosome 19q13.3 for prognosis of multiple myeloma patients after high-dose treatment and stem cell support: a linkage disequilibrium mapping in RAI and CD3EAP. (nih.gov)
The second strategy directly extracts haplotype linkage from the sequences of single chromosomes or sub-haploid chromosomal fragments ("molecular linkage") [ 6 ]. (biomedcentral.com)
The sparsity of haplotype linkage from Hi-C data limits its power to generate contiguous haplotypes [ 37 ] or accurately phase de novo mutations. (biomedcentral.com)
In contrast to previous methods that perform joint haplotype inference using linkage information from different technologies [ 37 - 39 ], we first determine high-confidence local haplotype blocks using linkage information from long-range/long-read sequencing and then merge these blocks into a single haplotype using Hi-C contacts. (biomedcentral.com)
In 1993, using genetic linkage, the gene for familial dysautonomia was localized to the distal long arm of chromosome 9(q31) with sufficient DNA markers to permit prenatal diagnosis and carrier identification for families in which an individual had been affected. (medscape.com)

The remarkable diversity of sex determination mechanisms known in fish may be fuelled by exceptionally high rates of sex chromosome turnovers or transitions. (nature.com)
The haplotype diversity for RM-Yplex haplotype is much more than the existing commercial Y-STR assays. (bl.uk)

P53 haplotypes defined by 3 polymorphisms (codon 72, intron 3, and intron 6) have been implicated in breast cancer]. (cdc.gov)
A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation. (snpedia.com)

1. Haplotype frequencies in a sub-region of chromosome 19q13.3, related to risk and prognosis of cancer, differ dramatically between ethnic groups. (nih.gov)
The haplotype frequencies in our control series (0.10) are similar to estimates made by Sjalander et al. (cdc.gov)
Analysis of the minor haplotype (H2) that caused recrudescence of Plasmodium malariae infection in a patient at Royal Darwin Hospital, Darwin, Northern Territory, Australia, March-April 2015, showing distribution of SNP alternative (nonreference) allele frequencies across the 14 chromosomes (boxes in the middle and dotted vertical lines) in the initial infection (bottom plot) and the recrudescence (top plot). (cdc.gov)

Haplotype ("haploid genotype") phase is the combination of genotypes at sites of genetic variation along a chromosome [ 1 ]. (biomedcentral.com)

3. Fine-mapping markers of lung cancer susceptibility in a sub-region of chromosome 19q13.3 among Chinese. (nih.gov)

Using SNP- and haplotype-based approaches, the effect of maternal smoking on wheezing was largest in children with the Ile105Val allele. (nih.gov)

The reasoning in doing so is twofold: first, language is an inherited cultural trait and thus the language phylae often correlate with genetic traits not the least to Y chromosome polymorphisms. (wikipedia.org)
A total of 16 haplotypes, each defined by a different combination of the various forms of each of these five restriction fragment length polymorphisms, were observed among the 44 scored individuals. (nih.gov)
Our recent studies used a novel, practical method to determine true extended haplotypes of these three polymorphisms in diploid genomes. (cdc.gov)

Of course, a Metapopulation concept on basis of "ethnicity" is by no means ideal, fully rational or fully translatable, but simply takes the fact into account that on a global level categories other than "nation" or "geography" far better describe the observed genetic clustering and inhomogeneity of Y chromosome patterns. (wikipedia.org)
Our results highlight the complexity of factors contributing to patterns observed in hybrid genomes, and we experimentally demonstrate that hybridisation can catalyze rapid evolution of a new sex chromosome. (nature.com)

98%) and assemble the syntenic structure of rearranged chromosomes in aneuploid cancer genomes at base pair level resolution. (biomedcentral.com)

In a previous study, we showed that an SNP tagging this haplotype (rs1800547) was associated with AD risk in a large population from the Dementia Genetics Spanish Consortium (DEGESCO) including 4435 cases and 6147 controls. (frontiersin.org)
A new study of mice by researchers from the Max Planck Institute for Molecular Genetics (MPIMG) in Berlin identifies a genetic factor called " t-haplotype ," whose tag-team act with the protein RAC1 helps a spermatozoan speed straight to the prize. (bigthink.com)
Genetics Home Reference (GHR) is a web-based resource for consumers that provides information about genetic conditions and the gene or chromosome variations that contribute to those conditions. (nih.gov)

There are two types: Y-chromosomes, inherited from your father, and mitochondrial DNA, inherited from your mother. (visionlearning.com)

The Y Chromosome Haplotype Reference Database (YHRD) is an open-access, annotated collection of population samples typed for Y chromosomal sequence variants. (wikipedia.org)
Because strong correlations exist between geographic areas and Y chromosomal variants, the YHRD population database was structured to display the geographic, linguistic and phylogenetic relationship of searched haplotype profiles. (wikipedia.org)
Interestingly, we identified a haplotype composed of the three minor variants as the third most common of 8 possible, with two haplotypes absent (analysis of >750 chromosomes). (cdc.gov)

Certain genetic sequences called haplotypes are passed on only by males or by females, so to get a complete picture of the ancestry of a population, scientists generate one family tree based on the male line and another based on the female line. (visionlearning.com)
Haplotypes are genetic sequences that we inherit from only one parent. (visionlearning.com)

Conventional analysis relies on either independent tests with each variant or the use of haplotypes in association analysis. (nih.gov)
Haplotypes that included both the promoter SNP (i.e., rs6591255) and the 105 Val variant were associated with an increased risk for asthma in non-Hispanic whites. (nih.gov)

Germ cells transition to meiosis, erase genomic imprints, and reactivate the X chromosome. (nih.gov)

In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. (snpedia.com)

Analysis of phylogenetic tree of the main haplotypes of sheep revealed that Zel breed was grouped in the haplotype B with other thin-tailed breeds, such as Karayaka and Sakiz. (researchgate.net)

HLA-DP haplotype analysis revealed a highly elevated PSC risk for HLA-DPA1*02:01~B1*01:01 (OR 1.99, p=6.7×10 −50 ). (bmj.com)

If there was no population structure in Africa, then we would expect to see this hX haplotype in different African locations. (blogspot.com)
One possible historical model that could generate this pattern supposes that differences between hX and other haplotypes arose in the presence of population structure that allowed for the divergence among Xp11.22 haplotypes. (blogspot.com)
Even if we discount the possibility of a non-African archaic human population as the source of hX, the age and low frequency of the haplotype does suggest a history in which hX persisted and diverged in a separate refugium population (either a separate modern human population or possibly an archaic human population). (blogspot.com)
The second, though it may increase power, often introduces uncertainty by estimating haplotypes from population data. (nih.gov)

Like the Y-chromosome Adam, she is, so to speak, the primordial mother of all humanity in pure maternal lineage. (igenea.com)
To accomplish this, we initially generated 104x genome coverage in PacBio Sequel long-read sequence from a single salmon male (Chromosome 3/6 Y lineage) from the St. John River broodstock of the USDA breeding program in Maine. (usda.gov)

The researchers conducted experiments with mouse sperm to learn more about the properties of the t-haplotype, a group of genetic alleles that are known to appear on Chromosome 17 of mice. (bigthink.com)

Taken together, these features of hX-that it is much older than other haplotypes and uncommon and patchily distributed throughout Africa, Europe, and Asia-present a cautionary tale for interpretations of human history. (blogspot.com)

This would be expected to result in selection for alternative sex chromosome systems in lineages arising from a hybridisation event. (nature.com)

Haplotype analysis findings confirmed high structural and allelic variations in IGHV1-69. (news-medical.net)

Fine mapping of the 17q candidate region defined the AIS critical region to be distal to marker D17S1806, spanning approximately 3.2 Mb on chromosome 17q25.3-qtel. (bmj.com)

2. HapMap-based study identifies risk sub-region on chromosome 19q13.3 in relation to lung cancer among Chinese. (nih.gov)

Similar effects were not detected in African-Americans or Hispanics, although the frequency of the 1-2-1 haplotype in the control patients was found to be higher 0.28 and 0.19, respectively than in Caucasian control patients (0.11). (cdc.gov)

The value of RM-Yplex was demonstrated for differentiating close male relatives in a case where a previously used Y-STR multiplex assay had shown identical haplotypes for those individuals. (bl.uk)

However, an examination of the different combinations of two or more allelic series suggests that some alleles are not randomly distributed and raises the possibility of establishing a genealogy of the human Y chromosome. (nih.gov)
This RFA builds on a previous RFA, HG-02-005 Large-Scale Genotyping for the Haplotype Map of the Human Genome ( https://grants.nih.gov/grants/guide/rfa-files/RFA-HG-02-005.html ). (nih.gov)
what's more, multiple copies of each chromosome also make the reconstruction of the potato genome a far greater technical challenge than was the case for the human genome. (mpg.de)

Our aim was to replicate our previous findings in an independent sample of 4124 AD cases and 3290 controls from Spain (GR@ACE project) and to analyze the effect of the H1 sub-haplotype structure on the risk of AD. (frontiersin.org)

A recent genetic study of Tibetan Y-chromosomes suggests that about 5,000-6,000 years ago, a subgroup of the Proto-Sino-Tibetan people, who had settled in the Yellow River valley, diverged from the ancestors of the Han Chinese and migrated, probably following the "Zang (Tibet)-Mien corridor," from the upper Yellow River region westward to Qinghai province and then southward to the Himalayas . (newworldencyclopedia.org)

Three QTL conferring resistance to FHB traits were detected on three chromosomes. (usda.gov)

Gene-pool structure of Tuvinians inferred from Y-chromosome marker data. (snpedia.com)

These data suggest that other endogenous or exogenous factors, perhaps related to race, contribute to breast cancer etiology in combination with this p53 haplotype. (cdc.gov)

We formulate both local haplotype inference and haplotype block concatenation as a minimization problem that can be efficiently solved by steepest descent methods. (biomedcentral.com)

The five polymorphic fragments map to Yq11, a region that does not recombine with the X chromosome and are therefore not redistributed. (nih.gov)
Conclusion: We demonstrate that GrASP makes it easier to visualize, summarize and prioritize regions of interest from sliding window haplotype analysis, based jointly on the p-value from all the tests from these windows and the building of haplotypes of significance in the region. (tmu.edu.tw)

Haplogroup N (Y-DNA) represents one of the twenty major branches of the Y chromosome as defined by the Y Chromosome Consortium (YCC2008). (snpedia.com)

Approximately 90-95% of patients have either DR3-DQ2 or DR5/7DQ2 haplotypes. (medscape.com)

Together, the seven most abundant haplotypes accounted for approximately 83% of HD chromosomes. (healthpartners.com)

Our work enables direct interrogation of chromosome-specific alterations and chromatin reorganization using bulk DNA sequencing. (biomedcentral.com)

A widely divergent haplotype of the X chromosome was found in Eurasians and East Africans but not at all in the Sub-Saharan Africans of the CEPH Panel. (blogspot.com)
Designated hX, this haplotype was found once in Melanesia (Oceania) and 8 times in widespread locations in Eurasia, including the Orkney Islands, Pakistan, Algeria, Israel, and France. (blogspot.com)

The Y-chromosome is passed on from father to son. (igenea.com)

Further, haplotype analysis was performed to identify alleles present on the chromosomes of the participants. (news-medical.net)

Most chromosome regions have only a few common haplotypes. (nih.gov)

Anatomy62

Organisms7

Diseases23

Chemicals and Drugs29

Analytical, Diagnostic and Therapeutic Techniques and Equipment27

Psychiatry and Psychology2

Phenomena and Processes165

Disciplines and Occupations4

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