Sentieon DNA pipeline for variant detection - Software-only solution, over 20× faster than GATK 3.3 with identical results

Weber, Jessica A.; Aldana, Rafael; Gallagher, Brendan D.; Edwards, Jeremy S.

doi:10.7287/peerj.preprints.1672v2

Cited by 29 publications

(26 citation statements)

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“…Mark duplication was performed with Sention (ref. 24; version 201611.02) on each BAM file. The reads were then realigned to the hg19 (GRCh37) genome with Sention to better identify the InDel mutations.…”

Section: Wgs Processingmentioning

confidence: 99%

Analysis of Mucosal Melanoma Whole-Genome Landscapes Reveals Clinically Relevant Genomic Aberrations

Zhou

Shi

Tao

et al. 2019

Clinical Cancer Research

140

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Purpose: Unlike advances in the genomics-driven precision treatment of cutaneous melanomas, the current poor understanding of the molecular basis of mucosal melanomas (MM) has hindered such progress for MM patients. Thus, we sought to characterize the genomic landscape of MM to identify genomic alterations with prognostic and/or therapeutic implications. Experimental Design: Whole-genome sequencing (WGS) was performed on 65 MM samples, including 63 paired tumor blood samples and 2 matched lymph node metastases, with a further droplet digital PCR-based validation study of an independent MM cohort (n ¼ 80). Guided by these molecular insights, the FDA-approved CDK4/6 inhibitor palbociclib was tested in an MM patient-derived xenograft (PDX) trial. Results: Besides the identification of well-recognized driver mutations of BRAF (3.1%), RAS family (6.2%), NF1 (7.8%), and KIT (23.1%) in MMs, our study also found that (i) mutations and amplifications in the transmembrane nucleoporin gene POM121 (30.8%) defined a patient subgroup with higher tumor proliferation rates; (ii) enrichment of structural variations between chromosomes 5 and 12 defined a patient subgroup with significantly worse clinical outcomes; (iii) over 50% of the MM patients harbored recurrent focal amplification of several oncogenes (CDK4, MDM2, and AGAP2) at 12q13-15, and this co-occurred significantly with amplification of TERT at 5p15, which was verified in the validation cohort; (iv) the PDX trial demonstrated robust antitumor effects of palbociclib in MMs harboring CDK4 amplification. Conclusions: Our largest-to-date cohort WGS analysis of MMs defines the genomic landscape of this deadly cancer at unprecedented resolution and identifies genomic aberrations that could facilitate the delivery of precision cancer treatments.

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Section: Wgs Processingmentioning

confidence: 99%

Analysis of Mucosal Melanoma Whole-Genome Landscapes Reveals Clinically Relevant Genomic Aberrations

Zhou

Shi

Tao

et al. 2019

Clinical Cancer Research

140

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“…Because P. stenoptera is equally related to all Juglans species, the reads from 80 individuals of Juglans were mapped to the P. stenoptera reference genome. SNPs from each individual were called and joined to create a multisample SNP data set using SENTIEON DNAseq software packages v. 201711.05 (Weber et al 2016). To control the quality of SNPs, triallelic and tetra-allelic SNP sites or sites with missing data or a mapping depth <10Â or >60Â in any individuals were removed.…”

Section: Sequencing Reads Mapping and Variant Callingmentioning

confidence: 99%

Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut

Zhang

et al. 2019

Molecular Biology and Evolution

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Persian walnut (Juglans regia) is cultivated worldwide for its high-quality wood and nuts, but its origin has remained mysterious because in phylogenies it occupies an unresolved position between American black walnuts and Asian butternuts. Equally unclear is the origin of the only American butternut, J. cinerea. We resequenced the whole genome of 80 individuals from 19 of the 22 species of Juglans and assembled the genome of its relatives Pterocarya stenoptera and Platycarya strobilacea. Using phylogenetic-network analysis of single-copy nuclear genes, genome-wide site pattern probabilities, and Approximate Bayesian Computation, we discovered that J. regia (and its landrace J. sigillata) arose as a hybrid between the American and the Asian lineages and that J. cinerea resulted from massive introgression from an immigrating Asian butternut into the genome of an American black walnut. Approximate Bayesian Computation modeling placed the hybrid origin in the late Pliocene, ∼3.45 My, with both parental lineages since having gone extinct in Europe.

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“…This was estimated based on the number of reads, expected sorghum genome size (732Mb), and read length. Variant calling was performed using Sentieon's DNAseq pipeline 201711.03 37 , a proprietary implementation of the GATK variant calling pipeline 38 . Briefly, BWA 39 version 0.7.13 was used to align the raw sequence reads to the BTx623 reference genome v3.1 available in Phytozome 18 .…”

Section: Sequencing and Variant Identificationmentioning

confidence: 99%

Comparative evolutionary analysis and prediction of deleterious mutation patterns between sorghum and maize

Lozano

Gazave

Santos

et al. 2019

Preprint

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Sorghum and maize share a close evolutionary history that can be explored through comparative genomics. To perform a large-scale comparison of the genomic variation between these two species, we analyzed 13 million variants identified from whole genome resequencing of 468 sorghum lines together with 25 million variants previously identified in 1,218 maize lines.Deleterious mutations in both species were prevalent in pericentromeric regions, enriched in non-syntenic genes, and present at low allele frequencies. A comparison of deleterious burden between sorghum and maize revealed that sorghum, in contrast to maize, departed from the "domestication cost" hypothesis that predicts a higher deleterious burden among domesticates compared to wild lines. Additionally, sorghum and maize population genetic summary statistics were used to predict a gene deleterious index with an accuracy higher than 0.5. This research represents a key step towards understanding the evolutionary dynamics of deleterious variants in sorghum and provides a comparative genomics framework to start prioritizing them for removal through genome editing and breeding. 2 Main text: Sorghum ( Sorghum bicolor L. Moench) and maize ( Zea mays L.) are both members of the Poaceae family and often serve as a model system for comparative plant genomics. Their common Poaceae ancestor underwent a whole-genome duplication (WGD) event ~96 million years ago 1 , and a second WGD in maize corresponds closely with its divergence 12 million years ago from sorghum 2 . The role of polyploidization in maize diversification 1 makes the sorghum-maize system particularly powerful for comparative studies.A rchaeobotanical studies support a single sorghum domestication event around 3000 BC in Eastern Sudan 3 , with genetic studies supporting a potential second independent domestication center in west Africa 4,5 . Maize, in contrast, was domesticated once from teosinte in the Balsas river valley in central Mexico around 9000 years ago 6,7 . While some orthologs between these two species experienced parallel selection during domestication 8 , most domestication related genes appear to be drawn from a non-overlapping set 9 . It is well established that maize experienced a decline in effective population size due to a domestication bottleneck 10,11 that increased the burden of deleterious alleles in the domesticate compared to teosinte 12,13 .Evidence for reduced nucleotide diversity in landraces from a genetic bottleneck 5 or population size decline 14 has also been reported for sorghum.Sorghum has a hermaphroditic inflorescence, contributing to its predominantly self-pollinating nature. Domesticated sorghum has an estimated outcrossing rate of only 7 to 20% 9,15 , while the outcrossing rate tends to be higher (up to 70% 16 ) for weedy and wild sorghum. In contrast, maize and its wild progenitor teosinte are monoecious and generally outcrossing at a rate of over 90% 17 . In this study, we performed a joint analysis of functional variation in sorghum and 3 maize lines that span th...

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Sentieon DNA pipeline for variant detection - Software-only solution, over 20× faster than GATK 3.3 with identical results

Cited by 29 publications

References 1 publication

Analysis of Mucosal Melanoma Whole-Genome Landscapes Reveals Clinically Relevant Genomic Aberrations

Analysis of Mucosal Melanoma Whole-Genome Landscapes Reveals Clinically Relevant Genomic Aberrations

Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut

Comparative evolutionary analysis and prediction of deleterious mutation patterns between sorghum and maize

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