human genomic dna reference material  (CapitalBio Corporation)

Journal: Cell genomics

Article Title: Benchmarking challenging small variants with linked and long reads

doi: 10.1016/j.xgen.2022.100128

Figure Lengend Snippet: Summary comparison of v.3.3.2 and v.4.2.1 HG002 benchmark sets

Article Snippet: DNA extracted from a single large batch of cells for 5 of the 7 genomes (HG001 to HG005) is publicly available in National Institute of Standards and Technology Reference Materials 8391 (HG002), 8392 (HG002-HG004), 8393 (HG005), and 8398 (HG001), available at https://www.nist.gov/srm .

Techniques:

Journal: Cell genomics

Article Title: Benchmarking challenging small variants with linked and long reads

doi: 10.1016/j.xgen.2022.100128

Figure Lengend Snippet: (A) Percentage of the genomic region that is included by HG002 v.3.3.2 and v.4.2.1 of all non-gap, autosomal GRCh38 bases; the MHC; low-mappability regions and segmental duplications; and 159 difficult-to-map, medically relevant genes described previously. (B) The number of unique SNVs by genomic context. Circle size indicates the total number of SNVs in the union of v.3.3.2 and v.4.2.1. Circles above the diagonal indicate a net gain of SNVs in the newer benchmark, and circles below the diagonal indicate a net loss of SNVs in the newer benchmark.

Article Snippet: DNA extracted from a single large batch of cells for 5 of the 7 genomes (HG001 to HG005) is publicly available in National Institute of Standards and Technology Reference Materials 8391 (HG002), 8392 (HG002-HG004), 8393 (HG005), and 8398 (HG001), available at https://www.nist.gov/srm .

Techniques:

Journal: Cell genomics

Article Title: Benchmarking challenging small variants with linked and long reads

doi: 10.1016/j.xgen.2022.100128

Figure Lengend Snippet: (A) Cumulative distribution of the percentage of each gene included in HG002 v.4.2.1 benchmark regions for 159 autosomal difficult-to-map, medically relevant genes. Dashed lines indicate that the number of genes included more than 90% increased from 19 in v.3.3.2 to 110 in v.4.2.1. (B) Pairwise comparison of difficult-to-map, medically relevant gene inclusion in the benchmark set. Genes falling on the dashed line are similarly included by both benchmark sets, whereas genes above (red fill) or below (blue fill) the dashed line are included more by the v.4.2.1 or v.3.3.2 benchmark set, respectively. The genes included more by v.4.2.1 tend to be in segmental duplications, and the smaller number of genes included more by v.3.3.2 are mostly genes duplicated in HG002 relative to GRCh38 and should be excluded.

Article Snippet: DNA extracted from a single large batch of cells for 5 of the 7 genomes (HG001 to HG005) is publicly available in National Institute of Standards and Technology Reference Materials 8391 (HG002), 8392 (HG002-HG004), 8393 (HG005), and 8398 (HG001), available at https://www.nist.gov/srm .

Techniques:

Journal: Cell genomics

Article Title: Benchmarking challenging small variants with linked and long reads

doi: 10.1016/j.xgen.2022.100128

Figure Lengend Snippet: Medically relevant genes in the KIR locus, such as KIR2DL1 , were partially included in v.3.3.2 with many erroneous variants but are correctly excluded by v.4.2.1 because of a likely duplication and other structural variation. Thick blue bars indicate regions included by each benchmark, and orange and light blue lines indicate positions of homozygous and heterozygous benchmark variants, respectively. A duplication of part of this region, which is common in the population, is supported by higher-than-normal coverage and high variant density across all technologies as well as alignment of multiple contigs from the maternal trio-based HG002 Hifiasm assembly (Hifiasm-maternal). The region is very challenging to characterize and assemble accurately because of high variability and copy number polymorphisms in the population as well as segmental duplications (shaded regions).

Article Snippet: DNA extracted from a single large batch of cells for 5 of the 7 genomes (HG001 to HG005) is publicly available in National Institute of Standards and Technology Reference Materials 8391 (HG002), 8392 (HG002-HG004), 8393 (HG005), and 8398 (HG001), available at https://www.nist.gov/srm .

Techniques: Variant Assay

Journal: Cell genomics

Article Title: Benchmarking challenging small variants with linked and long reads

doi: 10.1016/j.xgen.2022.100128

Figure Lengend Snippet: The medically relevant gene PMS2 is 85.6% included in the v.4.2.1 benchmark regions, whereas it is 25.9% included in v.3.3.2 because segmental duplications (shaded regions) were largely excluded in previous benchmark versions. Thick blue bars indicate regions included by each benchmark, and orange and light blue lines indicate positions of homozygous and heterozygous benchmark variants, respectively. This region is challenging for assembly-based approaches, and an extra contig from the maternal trio-based HG002 Hifiasm assembly (Hifiasm-maternal) aligned to the left half of the gene because of misalignment or misassembly.

Article Snippet: DNA extracted from a single large batch of cells for 5 of the 7 genomes (HG001 to HG005) is publicly available in National Institute of Standards and Technology Reference Materials 8391 (HG002), 8392 (HG002-HG004), 8393 (HG005), and 8398 (HG001), available at https://www.nist.gov/srm .

Techniques:

Journal: Cell genomics

Article Title: Benchmarking challenging small variants with linked and long reads

doi: 10.1016/j.xgen.2022.100128

Figure Lengend Snippet: Base pairs overlapping different types of difficult regions that are excluded from all input call sets for HG002

Article Snippet: DNA extracted from a single large batch of cells for 5 of the 7 genomes (HG001 to HG005) is publicly available in National Institute of Standards and Technology Reference Materials 8391 (HG002), 8392 (HG002-HG004), 8393 (HG005), and 8398 (HG001), available at https://www.nist.gov/srm .

Techniques: Variant Assay, Sequencing

Journal: Cell genomics

Article Title: Benchmarking challenging small variants with linked and long reads

doi: 10.1016/j.xgen.2022.100128

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: DNA extracted from a single large batch of cells for 5 of the 7 genomes (HG001 to HG005) is publicly available in National Institute of Standards and Technology Reference Materials 8391 (HG002), 8392 (HG002-HG004), 8393 (HG005), and 8398 (HG001), available at https://www.nist.gov/srm .

Techniques: Software, Sequencing