A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies—a whole-genome assembly and a regional chromosome assembly—were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional ∼12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Abstract:Objective: To investigate the distributions of human leukocyte antigen (HLA)-A and -B alleles and HLA-A-B haplotypes in the Yi ethnic minority of the Yunnan Province, situated in southwestern China. Methods: DNA typing for HLA-A and -B loci was performed using the polymerase chain reaction-sequence-based typing (PCR-SBT) method on 114 randomly selected healthy individuals of the Yi population. The allelic frequencies of HLA-A and -B loci were calculated by direct counting and HLA-A-B haplotypes were estimated using the expectation maximization algorithm.

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We have already coamplified minimal haplotypes (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II), two additional loci, namely, DYS438, DYS439, and Amelogenin, in a single PCR using the Y-PLEX 12 kit. We investigated 107 unrelated male individuals from the Uigur ethnic group and studied the allelic frequency distribution and haplotype diversity of 11 Y-chromosomal STRs. A number of 43 alleles (nine STR loci) and 27 phenotypes (including DYS385) were detected, with frequencies ranging from 0.0092 to 0.6296. A total of 103 haplotypes were identified, among which 99 were individual-specific and four haplotypes were found twice. The haplotype diversity for these 12 Y-STR loci was 0.9993.

In the present study, we investigated the genetic polymorphisms of 15 autosomal STR loci in the Russian population of northeastern Inner-Mongolia, China as well as its genetic relationships with other populations. DNA typing for 15 autosomal STR loci was performed on 148 randomly selected healthy individuals from the Russian population living in Eerguna, northeastern Inner-Mongolia. Allelic frequencies of these loci were calculated by direct counting. The genotype data of this Russian population was moreover compared to other populations using neighbor-joining method, as such constructing a phylogenic tree. A total of 143 alleles were found in the Russian population with corresponding allele frequencies in the range from 0.0034 to 0.5372. Among all the 15 loci, D18S51 had the highest polymorphism (PIC = 0.8632), whereas TPOX had the lowest (PIC = 0.5179). In the phylogenic tree, this Russian population has a close relationship with the populations of South Siberia and northeastern Asia. This study may increase our understanding of the genetic background of the Russian population in Eerguna, China as such providing useful information for anthropological research, forensic sciences as well as disease-association studies.