A definitive haplotype map of structural variations determined by microarray analysis of duplicated haploid genomes
نویسندگان
چکیده
Complete hydatidiform moles (CHMs) are tissues carrying duplicated haploid genomes derived from single sperms, and detecting copy number variations (CNVs) in CHMs is assumed to be sensitive and straightforward methods. We genotyped 108 CHM genomes using Affymetrix SNP 6.0 (GEO#: GSE18642) and Illumina 1 M-duo (GEO#: GSE54948). After quality control, we obtained 84 definitive haplotype consisting of 1.7 million SNPs and 2339 CNV regions. The results are presented in the database of our web site (http://orca.gen.kyushu-u.ac.jp/cgi-bin/gbrowse/humanBuild37D4_1/).
منابع مشابه
Haplotype Block Partitioning and tagSNP Selection under the Perfect Phylogeny Model
Single Nucleotide Polymorphisms (SNPs) are the most usual form of polymorphism in human genome.Analyses of genetic variations have revealed that individual genomes share common SNP-haplotypes. Theparticular pattern of these common variations forms a block-like structure on human genome. In this work,we develop a new method based on the Perfect Phylogeny Model to identify haplo...
متن کاملComparative bioinformatics analysis of a wild diploid Gossypium with two cultivated allotetraploid species
Background: Gossypium thurberi is a wild diploid species that has been used to improve cultivated allotetraploid cotton. G. thurberi belongs to D genome, which is an important wild bio-source for the cotton breeding and genetic research. To a certain degree, chloroplast DNA sequence information are a versatile tool for species identification and phylogenetic implications in plants. Different ch...
متن کاملA Dense Linkage Map for Chinook salmon (Oncorhynchus tshawytscha) Reveals Variable Chromosomal Divergence After an Ancestral Whole Genome Duplication Event
Comparisons between the genomes of salmon species reveal that they underwent extensive chromosomal rearrangements following whole genome duplication that occurred in their lineage 58-63 million years ago. Extant salmonids are diploid, but occasional pairing between homeologous chromosomes exists in males. The consequences of re-diploidization can be characterized by mapping the position of dupl...
متن کاملHaplotype sorting using human fosmid clone end-sequence pairs.
An important goal of human genetics and genomics is to understand the complete spectrum of genetic variation across a specific human haplotype. By combining information from a dense SNP map with fosmid end-sequence pairs (ESPs) aligned to the human genome reference sequence, we have developed a simple method to resolve human haplotypes using a previously developed clone resource. By partitionin...
متن کاملGlobal gene expression analysis using microarray to study differential vulnerability to neurodegeneration
Neurodegenerative disorders such as Parkinson’s disease, motor neuron disease and Alzheimer’s disease is characterized by loss of specific cells within certain regions of the brain. One of the most compelling questions is to determine why specific cell populations are vulnerable to neurodegeneration. We addressed this question by studying global gene expression changes using an animal model of ...
متن کامل