Scaling accurate genetic variant discovery to tens of thousands of samples

Poplin, Ryan; Ruano-Rubio,; Ma, DePristo; Tj, Fennell; Mo, Carneiro; Ga, Van der Auwera; De, Kling; Ld, Gauthier; Levy‐Moonshine, Ami; Roazen, David; Shakir, Khalid; Thibault, Joel; Chandran, Sahaana; Whelan, Christopher W.; Lek, M.; Gabriel, Stacey; Daly, Mark J.; Neale, Benjamin M.; MacArthur, Daniel G.; Banks, Eric

doi:10.1101/201178

Cited by 1,458 publications

(1,297 citation statements)

References 25 publications

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“…angsd is a package for SNP and genotype calling commonly used for whole genome data. angsd emphasizes the use of genotype likelihoods and probabilities rather than of explicit genotype calls, and is regarded as more accurate than GATK (Poplin et al, ) for the latter (Korneliussen et al, ; Maruki & Lynch, ). For SNP discovery, we found that Stacks had higher recall (Figure a,e; black vs. grey), but fractionally lower precision (Figure b,f; black vs. grey).…”

Section: Resultsmentioning

confidence: 99%

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

2019

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For half a century population genetics studies have put type II restriction endonucleases to work. Now, coupled with massively‐parallel, short‐read sequencing, the family of RAD protocols that wields these enzymes has generated vast genetic knowledge from the natural world. Here, we describe the first software natively capable of using paired‐end sequencing to derive short contigs from de novo RAD data. Stacks version 2 employs a de Bruijn graph assembler to build and connect contigs from forward and reverse reads for each de novo RAD locus, which it then uses as a reference for read alignments. The new architecture allows all the individuals in a metapopulation to be considered at the same time as each RAD locus is processed. This enables a Bayesian genotype caller to provide precise SNPs, and a robust algorithm to phase those SNPs into long haplotypes, generating RAD loci that are 400–800 bp in length. To prove its recall and precision, we tested the software with simulated data and compared reference‐aligned and de novo analyses of three empirical data sets. Our study shows that the latest version of Stacks is highly accurate and outperforms other software in assembling and genotyping paired‐end de novo data sets.

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Section: Resultsmentioning

confidence: 99%

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

2019

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“…The resulting alignment quality and statistics were checked using the Qualimap (v2.1.3) 52 and custom R (v3.4.1) scripts. Single nucleotide variants (both SNPs and InDels) were called using the GATK HaplotypeCaller (v3.5), 53 SAMtools (v1.4), and VarScan2 (v2.3.9) 54 according to published best practices recommend by developers of the tools. GATK (v3.5) base recalibration was applied during the variant calls.…”

Section: Illumina Miseq Data Analysismentioning

confidence: 99%

The major histocompatibility complex of Old World camelids: Class I and class I‐related genes

Plášil

Wijkmark

Elbers³

et al. 2019

HLA

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The genomic structure of the Major Histocompatibility Complex (MHC) region and variation in selected MHC class I related genes in Old World camels, Camelus bactrianus and Camelus dromedaries were studied. The overall genomic organization of the camel MHC region follows a general pattern observed in other mammalian species and individual MHC loci appear to be well conserved. Selected MHC class I genes B‐67 and BL3‐7 exhibited unexpectedly low variability, even when compared to other camel MHC class I related genes MR1 and MICA. Interspecific SNP and allele sharing are relatively common, and frequencies of heterozygotes are usually low. Such a low variation in a genomic region generally considered as one of the most polymorphic in vertebrate genomes is unusual. Evolutionary relationships between MHC class I related genes and their counterparts from other species seem to be rather complex. Often, they do not follow the general evolutionary history of the species concerned. Close evolutionary relationships of individual MHC class I loci between camels, humans and dogs were observed. Based on the results of this study and on our data on MHC class II genes, the extent and the pattern of polymorphism of the MHC region of Old World camelids differed from most mammalian groups studied so far. Camels thus seem to be an important model for our understanding of the role of genetic diversity in immune functions, especially in the context of unique features of their immunoglobulin and T‐cell receptor genes.

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“…12 Also, to eliminate most false-positive calls generated by artifacts from the sequencing process, we used the Genome Analysis Tool Kit (GATK) v3.5, including MarkDuplicate and LocalRealignment, 13 and then conducted hard filtering according to GATK recommendations. Because the NextSeq system generates base call (BCL) files aggregated by lane as raw data, we first converted the BCL files to FASTQ files using a bcl2fastq2 program provided by Illumina.…”

Section: Resultsmentioning

confidence: 99%

Genomic profiling of the residual disease of advanced high‐grade serous ovarian cancer after neoadjuvant chemotherapy

Kim

Shim

Bae

et al. 2019

Intl Journal of Cancer

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The goal of our study was to demonstrate the spectrum of genomic alterations present in the residual disease of patients with advanced high-grade serous ovarian cancer (HGSOC) after neoadjuvant chemotherapy (NAC), including matched pretreatment biopsies. During the study period between 2006 and 2017, we collected pre-NAC and post-NAC tumor tissue samples from patients with advanced HGSOC. We performed combined next-generation sequencing and immunohistochemistry to identify actionable targets and pathway activation in post-NAC residual tumors. We also examined whether post-NAC profiling of residual HGSOC identified targetable molecular lesions in the chemotherapy-resistant component of tumors. Among 102 post-NAC samples, 41 (40%) of patients had mutations in homologous recombination repair (HRR) genes (HRR deficiency). Patients with HRR mutations had higher tumor mutation burdens (p < 0.001) and higher alterations in the PI3K-AKT-mTOR pathway (p = 0.004) than patients without these HRR mutations. Nevertheless, we found no significant differences in progression-free survival (p = 0.662) and overall survival (OS; p = 0.828) between the two groups. Most patients (91%) had alterations in at least one of the targetable pathways, and those patients with cell cycle (p = 0.004) and PI3K-AKT-mTOR signaling (p = 0.005) pathway alterations had poorer OS (Bonferroni-corrected threshold = 0.0083, 0.05/6). We showed the genomic landscape of tumor cells remaining in advanced HGSOC after NAC. Once validated, these data can help inform biomarker-driven adjuvant studies in targeting residual tumors to improve the outcomes of patients with advanced HGSOC after NAC.

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Scaling accurate genetic variant discovery to tens of thousands of samples

Cited by 1,458 publications

References 25 publications

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

The major histocompatibility complex of Old World camelids: Class I and class I‐related genes

Genomic profiling of the residual disease of advanced high‐grade serous ovarian cancer after neoadjuvant chemotherapy

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