• By using two sequencing primers with 3'end corresponding to the two alleles in a given SNP locus, we are able to obtain allele-specific DNA sequences from both alleles. (nofima.no)
  • Our algorithm will be useful for haplotyping of rare alleles and studies of allele-specific somatic aberrations. (nsf.gov)
  • Our results show unequivocal characterization of all alleles present, validated by correspondence against confirmed HLA database entries and haplotyping results from previous studies. (scilifelab.se)
  • Here we present 4.25 Mb of the human haplotype QBL (HLA-A26-B18-Cw5-DR3-DQ2) and compare it with the MHC reference haplotype and with a second haplotype, COX (HLA-A1-B8-Cw7-DR3-DQ2), that shares the same HLA-DRB1, -DQA1, and -DQB1 alleles. (ox.ac.uk)
  • A haplotype ( haploid genotype ) is a group of alleles in an organism that are inherited together from a single parent. (wikipedia.org)
  • First, it is used to mean a collection of specific alleles (that is, specific DNA sequences) in a cluster of tightly linked genes on a chromosome that are likely to be inherited together-that is, they are likely to be conserved as a sequence that survives the descent of many generations of reproduction. (wikipedia.org)
  • 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)
  • Dr. Scheet's lab has helped pioneer methods to more accurately distinguish these alterations using information on the order of inherited alleles on a chromosome, i.e. the haplotypes. (mdanderson.org)
  • Upstream sequences were also identified for a set of previously uncharacterized germline gene alleles. (lu.se)
  • Finally, based on the outcomes of the analysis, we define a set of testable hypotheses with respect to the placement of particular alleles in complex IGHV locus haplotypes, and discuss the evolutionary relatedness of particular heavy chain variable genes based on sequences of their upstream regions. (lu.se)
  • In a previous study, several HLA-B and HLA-C alleles and haplotypes were positively or negatively associated with the occurrence and prognosis of glioblastoma multiforme (GBM). (cdc.gov)
  • Molecular data have been an integral tool in the resolution of the evolutionary relationships and systematics of freshwater mussels, despite the limited number of nuclear markers available for Sanger sequencing. (mdpi.com)
  • The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. (springer.com)
  • PCR and Sanger sequencing were used to confirm mutations in and screen other family members where they were available. (molvis.org)
  • Sanger sequencing was used to perform the cosegregation analysis. (molvis.org)
  • Compared with traditional Sanger sequencing, targeted NGS for genetic testing of congenital cataracts markedly increases the mutation detection rate and is cost-effective. (molvis.org)
  • Previous studies regarding gene mutations in congenital cataracts have used Sanger sequencing in known disease-causing genes. (molvis.org)
  • After completing a B.A. in Biology, Dr. Scheet worked on the Human Genome Project at the Genome Center at Washington University in St. Louis, performing Sanger sequencing and informatics. (mdanderson.org)
  • Sanger dideoxy sequencing ##Assembly-Data-END## FEATURES Location/Qualifiers source 1. (cdc.gov)
  • Data produced with short-read sequencing technologies result in ambiguous haplotyping and a limited capacity to investigate the full repertoire of biologically relevant forms of genetic variation. (scilifelab.se)
  • Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. (genomeweb.com)
  • Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. (genomeweb.com)
  • Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history. (ox.ac.uk)
  • For the future direction, we need the in-depth genome sequence information and analysis for most of the mammals, including human to fully understand genome variation of economic traits, genetic susceptibility to diseases, and pharmacogenomics of drug response. (springer.com)
  • Genetic testing was performed on peripheral blood samples, by sequencing the coding regions of SCN1A bidirectionally and using MLPA (Multiplex Ligation dependent Probe Amplification), as previously described by Depienne et al. (hindawi.com)
  • This study reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems. (elifesciences.org)
  • Highly accurate long-read HiFi sequencing data for five complex genomes. (crossref.org)
  • Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. (crossref.org)
  • Modern high-throughput metagenomics is producing hundreds of thousands of metagenome-assembled genomes (MAGs), which is overwhelming traditional sequence-similarity search methods. (nature.com)
  • Reducing assembly complexity of microbial genomes with single-molecule sequencing. (speakerdeck.com)
  • With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. (springer.com)
  • During this period, tremendous success has been achieved in the fields of decoding of human genome, technological advancement of new era of human genome applications, toward personalized genomes and discovery of rare variants, leveraging genome sequencing to impact on cancer researches and mammalian evolution and population structure. (springer.com)
  • 2009): Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes. (boku.ac.at)
  • We here present a scalable and affordable protocol for the enrichment of long genomic fragments of blood group loci for long read sequencing. (isbtweb.org)
  • We achieve high sequencing coverage for desired blood group loci, can reliably phase heterozygous SNPs and leverage the advantages of long reads for accurate SNP and structural variation detection. (isbtweb.org)
  • To demonstrate the utility of these markers, we provide haplotype networks, DNA alignments, and summary statistics regarding the sequence variation for the two protein-coding nuclear loci (FEM1 and UbiA). (mdpi.com)
  • Sex-determining regions (SDRs) or mating-type (MT) loci in two sequenced volvocine algal species, Chlamydomonas reinhardtii and Volvox carteri, exhibit major differences in size, structure, gene content, and gametolog differentiation. (wustl.edu)
  • Thousands of loci were found in each genome where reads spanning 2 or 3 SNPs displayed more than two haplotypes, indicating that the locus is heterogeneous. (biomedcentral.com)
  • We have defined the complete gene, splice variant, and sequence variation contents of all three haplotypes, comprising over 259 annotated loci and over 20,000 single nucleotide polymorphisms (SNPs). (ox.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 do not know which haplotype you have, e.g. (wikipedia.org)
  • Advancement in identification of MHC genes that confer susceptibility to disease requires greater knowledge of sequence variation across the complex. (ox.ac.uk)
  • Using the diploid assembly to assess haplotype variation, we discovered genes under positive selection enriched for stress-response, growth,and flowering functions. (usda.gov)
  • Thirty-four known candidate genes for congenital cataracts were analyzed in the probands of 21 families with targeted next-generation sequencing (NGS). (molvis.org)
  • We studied the class II genes in these chicken strains and determined that: 1) the lines expressed from 1-3 class II genes, and 2) each line had a unique sequence form of each expressed gene. (usda.gov)
  • By defining the sequence forms of these and other MHC genes it will be possible to clarify if both class I and II genes are relevant in disease resistance, and to predict which form(s) of these gene(s) determine resistance to a disease. (usda.gov)
  • Upstream and downstream sequences of immunoglobulin genes may affect the expression of such genes. (lu.se)
  • Current diagnostic PCR assays target a variety of SARS CoV-2 genes and the vast majority target sequences in regions of the SARS CoV-2 genome that are highly conserved. (who.int)
  • This study also examined the mitochondrial DNA haplotype diversity of A. interioris , as it could contribute to our understanding of the biogeography and life history of this eel species. (scielo.br)
  • Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage. (genomeweb.com)
  • World-wide phylogeographic distribution of human complete mitochondrial DNA sequences suggested a West Asian origin for the autochthonous North African lineage U6. (nih.gov)
  • Divergence times, geographic origin and expansions of the U6 mitochondrial DNA clade, have been deduced from the analysis of 14 complete U6 sequences, and 56 different haplotypes, characterized by hypervariable segment sequences and RFLPs. (nih.gov)
  • Our results highlight the need for new methods to analyze genomic variation because existing ones do not systematically consider local haplotypes. (biomedcentral.com)
  • These results indicate that the differential disease associations of these two DR3 haplotypes are due to sequence variation outside this central 158-kb segment, and that shuffling of ancestral blocks via recombination is a potential mechanism whereby certain DR-DQ allelic combinations, which presumably have favoured immunological functions, can spread across haplotypes and populations. (ox.ac.uk)
  • Comparative analysis of haplotypes provides insight into large-scale structural variation and the selective pressures that have driven hop evolution. (usda.gov)
  • The methods treated cover a large number of topics from traditional population genetics to large-scale genomics with high-throughput sequencing data. (routledge.com)
  • We describe a statistical test to measure concurrent allele dropout between single-nucleotide polymorphisms (SNPs) across multiple sequenced single cells. (nsf.gov)
  • Starting with the assumption that a single NGS read (or read pair) must come from one haplotype, we built a procedure for directly observing haplotypes at a local level by examining 2 or 3 adjacent single nucleotide polymorphisms (SNPs) which are close enough on the genome to be spanned by individual reads. (biomedcentral.com)
  • represents the sequence between the SNPs - which is common to all four), based on what combinations of bases are found on a DNA strand. (biomedcentral.com)
  • If individual reads span both SNPs, then these combinations are directly observable and it is possible to list haplotypes. (biomedcentral.com)
  • SNPs representing several sequence variants were identified from population data. (lu.se)
  • The B gene expressed at each locus in each line had unique DNA sequences from the B gene expressed in other lines. (usda.gov)
  • Only the B-LBII locus was expressed in all haplotypes. (usda.gov)
  • The Y Chromosome Haplotype Reference Database (YHRD) is an open-access, annotated collection of population samples typed for Y chromosomal sequence variants. (wikipedia.org)
  • To address this issue, we are employing a bacterial artificial chromosome (BAC) cloning strategy to sequence entire MHC haplotypes from consanguineous cell lines as part of the MHC Haplotype Project. (ox.ac.uk)
  • It can be all the chromosomes from one of the parents or a minor part of a chromosome, for example a sequence of 9000 base pairs . (wikipedia.org)
  • Haplotype analysis revealed a chromosome region of 475 kb containing the mutation in the GJA8 gene was harbored by two families. (molvis.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)
  • Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans. (genomeweb.com)
  • Bioinformatics analysis of the sequence variants was performed through computational predictive programs. (molvis.org)
  • Several novel upstream region variants were validated, for instance by their segregation to a single haplotype in heterozygotic subjects. (lu.se)
  • We evaluated this direct haplotype-specific approach by determining haplotypes within the intron 2 sequence of the fructan-6-fructosyltransferase (6-ft) gene in Lolium perenne L. We obtained reliable haplotype-specific sequences for all primers and genotypes evaluated. (nofima.no)
  • Four of these autosome-to-Y gene copies became inactivated ("pseudogenes"), lost part of their sequences, and most likely will disappear in the next few million years. (speakerdeck.com)
  • Here, we report a study on gene sequencing of the SCN1A gene in eight Lebanese cases with Dravet syndrome. (hindawi.com)
  • Genotyping and haplotype analyses were performed in two patients with a p.V44M mutation in the GJA8 gene. (molvis.org)
  • Using long sequencing reads from the Oxford Nanopore Technologies platform, we phased SNVs within large gene copy arrays for the first time. (elifesciences.org)
  • Following duplication events, the resulting stretches of homologous sequence can promote recombination between gene copies. (elifesciences.org)
  • or the transmembrane protein gene cassettes of some pathogenic bacteria ( Santoyo and Romero, 2005 ), gene conversion can also generate sequence diversity. (elifesciences.org)
  • We conclude that the haplotype-specific sequencing is robust, and that the approach has a potentially very wide application range for any diploid organism. (nofima.no)
  • 7546 /organism="Norovirus GII/Hu/HK/2016/GII.P16_GII.2/CUHK-NS-1082" /mol_type="genomic RNA" /strain="CUHK-NS-1082" /db_xref="taxon:1971450" /haplotype="Homo sapiens" /country="Hong Kong" /collection_date="21-Sep-2016" /note="genotype: GII.P16_GII.2" CDS 5. (cdc.gov)
  • These methods work by applying the observation that certain haplotypes are common in certain genomic regions. (wikipedia.org)
  • We show that amplification biases have a potential upside: long-range correlations in rates of allele dropout provide a signal for phasing haplotypes at the lengths of amplicons from WGA, lengths which are generally longer than than individual sequence reads. (nsf.gov)
  • Barcode-based clustering of sequencing reads confirmed analysis of over 2000 independently assayed template molecules, with an average of 753 reads in support of called polymorphisms. (scilifelab.se)
  • Haplotype estimation using sequencing reads. (genomeweb.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)
  • We introduce the technique of Local Haplotyping Analysis (LHA) which shows that evidence for heterogeneity is strong and directly observable in Next Generation Sequencing (NGS) data. (biomedcentral.com)
  • A comparison of next-generation sequencing and clone-based sequencing in analysis of HBV RT quasispecies heterogeneity. (genomeweb.com)
  • Analysis of the two DR3 haplotypes allowed delineation of the shared sequence between two HLA class II-related haplotypes differing in disease associations and the identification of at least one of the sites that mediated the original recombination event. (ox.ac.uk)
  • Microsatellite genotyping was used for haplotype analysis. (molvis.org)
  • Cruz Garcia Rodriguez Address Unidad de Inmunologia, Hospital La Paz, Paseo de Address la Castellana 261, 28046 Madrid, Spain Telephone +34-91-7277095 Fax +34-91-7277095 Email [email protected] Method SSCP, Direct sequencing Frequency Whenever required Samples 2 samples per year Prices 300 EUR/patient 112/carrier Comment Patient samples are only accepted for analysis after Comment prior consultation and submission of clinical and Comment laboratory data. (lu.se)
  • Novel CIC point mutations and an exon-spanning, homozygous deletion identified in oligodendroglial tumors by a comprehensive genomic approach including transcriptome sequencing. (genomeweb.com)
  • 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)
  • However, this dramatically improved after performing genotyping-by-sequencing in the first round of selfing, followed by high-resolution-melting single nucleotide polymorphism genotyping in subsequent selection steps. (frontiersin.org)
  • [8] A haplogroup is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation . (wikipedia.org)
  • However, it is possible to estimate the probability of a particular haplotype when phase is ambiguous using a sample of individuals. (wikipedia.org)
  • Region-wide F ST and cross-population-extended haplotype homozygosity (XP-EHH) between DSN and Holstein were used to detect selection signatures between the two breeds, and RoH islands were used to detect selection signatures within DSN and Holstein. (frontiersin.org)
  • This research is the first report of a draft genome of a diploid plant whereby DNA sequences from both the mother and father are reported. (usda.gov)
  • Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions. (cdc.gov)
  • PacBio long-read sequences from hop were assembled with FALCON and phased with FALCON-Unzip. (usda.gov)
  • The submissions are then registered to the public database, where the entries are retrievable by Search for haplotypes, contributors or accession numbers. (wikipedia.org)
  • A. Brooimans Address Wilhelmina Children's Hospital Dept. of Immunology Address Lundlaan 6, 3584 EA Utrecht, The Netherlands Telephone +31-302504354 Fax +31-302505311 Email [email protected] Method Direct sequencing Turnaround 1 month Samples 8 // Disease Wiskott-Aldrich syndrome and X-linked thrombocytopenia Accession I0009 Date 17-Dec-1999 (Rel. (lu.se)
  • ABSTRACT A diagnostic polymerase chain reaction (PCR) assay using species-specific primers and direct sequencing was used to identify members of the Anopheles maculipennis complex in the north-west and central regions of the Islamic Republic of Iran. (who.int)
  • InsertionMapper: a pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. (genomeweb.com)
  • The completion of the first human genome drafts (Yamey 2000 ) was just a start of the modern DNA sequencing era which resulted in further invention, improved development toward new advanced strategies of high-throughput DNA sequencing, so called the " high-throughput next generation sequencing " (HT-NGS). (springer.com)
  • This can only be achieved with comprehensive and haplotype-resolved data generated by third-generation long read sequencing. (isbtweb.org)
  • Unfortunately, WGA introduces biases in the resulting sequencing data, including non-uniformity in genome coverage and high rates of allele dropout. (nsf.gov)
  • However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. (nsf.gov)
  • We show that heterogeneity is in fact ubiquitous and readily observable in ordinary Next Generation Sequencing (NGS) data. (biomedcentral.com)
  • An evaluation of allele frequency estimation accuracy using pooled sequencing data. (genomeweb.com)
  • Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data. (genomeweb.com)
  • Variant callers for next-generation sequencing data: a comparison study. (genomeweb.com)
  • This model approximated important features of the established "coalescent" model but allowed for computationally efficient inference of important features, such as haplotypes and missing genotypes from panels of reference data. (mdanderson.org)
  • Inference from large, rearranged immunoglobulin transcriptome data sets offers an opportunity to define the upstream regions (5'-untranslated regions and leader sequences). (lu.se)
  • We report the methods used for marker development, along with the primer sequences and optimized PCR and thermal cycling conditions. (mdpi.com)
  • Therefore, given a set of possible haplotype resolutions, these methods choose those that use fewer different haplotypes overall. (wikipedia.org)
  • The objective of this document is to outline the available methods and tools for screening and sequencing patient specimens for the detection of VOC or VOI, with a focus on those that offer a rapid turn-around time so as to support rapid implementation of public health actions for COVID 19 control. (who.int)
  • We use results of this test to perform haplotype assembly across a collection of single cells. (nsf.gov)
  • Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. (crossref.org)
  • Phased diploid genome assembly with single-molecule real-time sequencing. (crossref.org)
  • We present the first report of a haplotype-phased assembly of a large plant genome. (usda.gov)
  • However, no simple and robust approaches are currently available for determining haplotype-specific sequence information. (nofima.no)
  • Also involving business principles, Tim seeks to translate effective research approaches and to develop affordable applications of sequencing in precision medicine for the benefit of patients. (isbtweb.org)
  • 2003 ). The NHGRI has categorized new sequencing approaches into those that offer near-term and revolutionary benefits with a 100-fold cost reduction per base pair (bp) within the next five years. (springer.com)
  • Current technologies for single-cell DNA sequencing require whole-genome amplification (WGA), as a single cell contains too little DNA for direct sequencing. (nsf.gov)
  • The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing. (genomeweb.com)
  • RESUME Une PCR (amplification en chaîne par polymérase) diagnostique avec des amorces spécifiques d'espèces et un séquençage direct ont été utilisés pour la détermination des membres du complexe Ano- pheles maculipennis dans les régions du nord-ouest et du centre de la République islamique d'Iran. (who.int)
  • Specimens were collected from 9 provinces during 2 seasonal activities in 2001-2002, identified morphologically and subjected to PCR assay and direct sequencing. (who.int)
  • Here we describe Droplet Barcode Sequencing, a novel approach for creating linked-read sequencing libraries by uniquely barcoding the information within single DNA molecules in emulsion droplets, without the aid of specialty reagents or microfluidic devices. (scilifelab.se)
  • Real-time DNA sequencing from single polymerase molecules. (crossref.org)
  • DNA sequencing using electrical conductance measurements of a DNA polymerase. (genomeweb.com)
  • Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules. (scilifelab.se)
  • Instead of having a C/T heterozygous SNP uniformly, the sequenced tissue might be heterogeneous and consist of two different cell lineages: one of which is homozygous for C and the other homozygous for T. Direct evidence to support such an alternate hypothesis cannot be found when examining a single genomic site. (biomedcentral.com)
  • Additional evaluation of HLA-A promoter and exon 1 sequences did not detect any unexpected single nucleotide polymorphisms that could suggest differential allelic expression. (cdc.gov)
  • Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons. (genomeweb.com)
  • Our molecular analyses showed the presence of the same haplotypes along the different locations in the Indo-Pacific region. (scielo.br)
  • Further analyses restricted to female GBM cases and controls revealed a second association with a specific HLA-B sequence motif corresponding to Bw4-80Ile (odds ratio = 2.71, p = 0.02). (cdc.gov)
  • 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)
  • Des spécimens ont été capturés dans 9 provinces pendant deux activités saisonnières en 2001-2002, identifiés morphologiquement et soumis à une PCR et à un séquençage direct. (who.int)
  • Instead, we examine all possible haplotypes with the explicit aim of evaluating evidence for heterogeneity in the tissue. (biomedcentral.com)
  • We have addressed this problem by developing a very simple and robust haplotype-specific sequencing approach. (nofima.no)
  • With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is nearly 78% repetitive. (usda.gov)