Posts Tagged ‘Haplotype’

De novo assembly and phasing of a Korean human genome

Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.

DNA barcoding reveals polymorphism in the pygmy grasshopper Tetrix bolivari (Orthoptera, Tetrigidae)

ZooKeys 582: 111-120
DOI: 10.3897/zookeys.582.6301
Authors: Ling Zhao, Li-Liang Ling, Zhe-Min Zheng
Abstract: Many pygmy grasshopper species exhibit colour-marking polymorphism. However, this polymorphism in some species, such as T…

Novel Haplotype Tagging Single Nucleotide Polymorphisms and Use of Same to Predict Childhood Lymphoblastic Leukemia

The present invention is directed to novel haplotype tagging single nucleotide polymorphisms (SNPs) in specific regions outside the HFE gene that serve as a reliable biomarker for a decreased risk for childhood lymphoblastic leukemia (ALL) in a child. …

METHODS OF IMPROVING APHID RESISTANCE IN SOYBEANS

This invention relates to methods of improving resistance to aphids in soybean plants, as well as methods for identifying and/or selecting soybean plants or germplasm that display improved resistance to one or more biotypes of soybean aphid. In certain…

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