21 Result(s)
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Yumi Yamaguchi-Kabata
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Article
Linkage of Amino Acid Variation and Evolution of Human Immunodeficiency Virus Type 1 gp120 Envelope Glycoprotein (Subtype B) with Usage of the Second Receptor
To clarify the relationship between the amino acid variations of the gp120 of human immunodeficiency virus type 1 (HIV-1) and the chemokine receptors that are used as the second receptor for HIV, we evaluated ...
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Article
Open AccessiSVP: an integrated structural variant calling pipeline from high-throughput sequencing data
Structural variations (SVs), such as insertions, deletions, inversions, and duplications, are a common feature in human genomes, and a number of studies have reported that such SVs are associated with human di...
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Chapter and Conference Paper
SVEM: A Structural Variant Estimation Method Using Multi-mapped Reads on Breakpoints
Recent development of next generation sequencing (NGS) technologies has led to the identification of structural variants (SVs) of genomic DNA existing in the human population. Several SV detection methods util...
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Chapter and Conference Paper
HapMonster: A Statistically Unified Approach for Variant Calling and Haploty** Based on Phase-Informative Reads
Haplotype phasing is essential for identifying disease-causing variants with phase-dependent interactions as well as for the coalescent-based inference of demographic history. One of approaches for estimating ...
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Article
Open AccessHuman genetic research, race, ethnicity and the labeling of populations: recommendations based on an interdisciplinary workshop in Japan
A challenge in human genome research is how to describe the populations being studied. The use of improper and/or imprecise terms has the potential to both generate and reinforce prejudices and to diminish the...
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Article
Open AccessSUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing
Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by tec...
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Article
Open AccessValidation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population
Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers fo...
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Article
Open AccessTIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads
High-throughput RNA sequencing (RNA-Seq) enables quantification and identification of transcripts at single-base resolution. Recently, longer sequence reads become available thanks to the development of new ty...
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Article
Open AccessHLA-VBSeq: accurate HLA ty** at full resolution from whole-genome sequencing data
Human leucocyte antigen (HLA) genes play an important role in determining the outcome of organ transplantation and are linked to many human diseases. Because of the diversity and polymorphisms of HLA loci, HLA...
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Article
Open AccessEstimating copy numbers of alleles from population-scale high-throughput sequencing data
With the recent development of microarray and high-throughput sequencing (HTS) technologies, a number of studies have revealed catalogs of copy number variants (CNVs) and their association with phenotypes and ...
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Article
Open AccessRare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals
The Tohoku Medical Megabank Organization reports the whole-genome sequences of 1,070 healthy Japanese individuals and construction of a Japanese population reference panel (1KJPN). Here we identify through thi...
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Article
Open AccessiJGVD: an integrative Japanese genome variation database based on whole-genome sequencing
The integrative Japanese Genome Variation Database (iJGVD; http://ijgvd.megabank.tohoku.ac.jp/) provides genomic variation data detected by whole-genome sequ...
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Article
Open AccessThe structural origin of metabolic quantitative diversity
Relationship between structural variants of enzymes and metabolic phenotypes in human population was investigated based on the association study of metabolite quantitative traits with whole genome sequence dat...
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Article
Selection pressure on human STR loci and its relevance in repeat expansion disease
Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units...
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Article
Open AccessIntegrated analysis of human genetic association study and mouse transcriptome suggests LBH and SHF genes as novel susceptible genes for amyloid-β accumulation in Alzheimer’s disease
Alzheimer’s disease (AD) is a common neurological disease that causes dementia in humans. Although the reports of associated pathological genes have been increasing, the molecular mechanism leading to the accu...
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Article
Open AccessRegional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project
Genotype imputation from single-nucleotide polymorphism (SNP) genotype data using a haplotype reference panel consisting of thousands of unrelated individuals from populations of interest can help to identify ...
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Article
Estimating carrier frequencies of newborn screening disorders using a whole-genome reference panel of 3552 Japanese individuals
Incidence rates of Mendelian diseases vary among ethnic groups, and frequencies of variant types of causative genes also vary among human populations. In this study, we examined to what extent we can predict p...
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Article
Open Access3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome
The first step towards realizing personalized healthcare is to catalog the genetic variations in a population. Since the dissemination of individual-level genomic information is strictly controlled, it will be...
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Article
Open AccessEstimation of the carrier frequencies and proportions of potential patients by detecting causative gene variants associated with autosomal recessive bone dysplasia using a whole-genome reference panel of Japanese individuals
Bone dysplasias are a group of rare hereditary diseases, with up to 436 disease types. Perinatal diagnosis is clinically important for adequate personalized management and counseling. There are no reports focu...
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Article
Open AccessPathological variants in genes associated with disorders of sex development and central causes of hypogonadism in a whole-genome reference panel of 8380 Japanese individuals
Disorders of sex development (DSD) comprises a congenital condition in which chromosomal, gonadal, or anatomical sex development is atypical. In this study, we screened for pathogenic variants in 32 genes asso...
