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.1672v1

Cited by 20 publications

(17 citation statements)

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“…Variant Detection Gene variant refer to changes in the base of genome, including point mutations caused by single base changes, or deletions, duplications, or insertions of multiple bases. In this analysis, the workflow of Sentieon 58…”

Section: Whole Exome Sequencing Data Preprocessingmentioning

confidence: 99%

The genetic determinants of language network dysconnectivity in drug-naïve early stage schizophrenia

Palaniyappan

Liu

et al. 2021

npj Schizophr

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Schizophrenia is a neurocognitive illness of synaptic and brain network-level dysconnectivity that often reaches a persistent chronic stage in many patients. Subtle language deficits are a core feature even in the early stages of schizophrenia. However, the primacy of language network dysconnectivity and language-related genetic variants in the observed phenotype in early stages of illness remains unclear. This study used two independent schizophrenia dataset consisting of 138 and 53 drug-naïve first-episode schizophrenia (FES) patients, and 112 and 56 healthy controls, respectively. A brain-wide voxel-level functional connectivity analysis was conducted to investigate functional dysconnectivity and its relationship with illness duration. We also explored the association between critical language-related genetic (such as FOXP2) mutations and the altered functional connectivity in patients. We found elevated functional connectivity involving Broca’s area, thalamus and temporal cortex that were replicated in two FES datasets. In particular, Broca’s area - anterior cingulate cortex dysconnectivity was more pronounced for patients with shorter illness duration, while thalamic dysconnectivity was predominant in those with longer illness duration. Polygenic risk scores obtained from FOXP2-related genes were strongly associated with functional dysconnectivity identified in patients with shorter illness duration. Our results highlight the criticality of language network dysconnectivity, involving the Broca’s area in early stages of schizophrenia, and the role of language-related genes in this aberration, providing both imaging and genetic evidence for the association between schizophrenia and the determinants of language.

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Section: Whole Exome Sequencing Data Preprocessingmentioning

confidence: 99%

The genetic determinants of language network dysconnectivity in drug-naïve early stage schizophrenia

Palaniyappan

Liu

et al. 2021

npj Schizophr

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“…The preprocessed reads were aligned to the reference human genome (GRCh38) downloaded from UCSC Database (Meyer et al, 2013) using BWA-mem (Li & Durbin, 2010). Aligned read processing and variant calling steps were performed using the Sentieon version of GATK (Weber et al, 2016). Briefly, the aligned reads were sorted and duplicate reads were removed.…”

Section: Data Processing and Germline Variant Callingmentioning

confidence: 99%

“…Base quality score recalibration (BQSR) was done using known variants from dbsnp (version 149). Germline variant calling was performed using the Haplotyper command in Sentieon (Weber et al, 2016).…”

Section: Data Processing and Germline Variant Callingmentioning

confidence: 99%

Matrilineal analysis of mutations in the DMD gene in a multigenerational South Indian cohort using DMD gene panel sequencing

Shastry¹,

Aravind

Sunil

et al. 2021

Molec Gen & Gen Med

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“…The pre-processed reads were aligned to the reference human genome (hg19, Feb. 2009 release) downloaded from UCSC Database 10 using BWA-mem 11 . Aligned read processing and variant calling steps were performed using Sentieon version of GATK 12 . Briefly, the aligned reads were sorted, and duplicate reads were removed.…”

mentioning

confidence: 99%

“…Base quality score recalibration (BQSR) was done using known variants from dbSNP (v149). The germline variant calling was performed using Haplotyper command in Sentieon 12 .…”

mentioning

confidence: 99%

Phenotypic expression and clinical outcomes in a South Asian PRKAG2 cardiomyopathy cohort

Ahamed

Balegadde

Menon

et al. 2020

Sci Rep

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The PRKAG2 syndrome is a rare autosomal dominant phenocopy of sarcomeric hypertrophic cardiomyopathy (HCM), characterized by ventricular pre-excitation, progressive conduction system disease and left ventricular hypertrophy. This study describes the phenotype, genotype and clinical outcomes of a South-Asian PRKAG2 cardiomyopathy cohort over a 7-year period. Clinical, electrocardiographic, echocardiographic, and cardiac MRI data from 22 individuals with PRKAG2 variants (68% men; mean age 39.5 ± 18.1 years), identified at our HCM centre were studied prospectively. At initial evaluation, all of the patients were in NYHA functional class I or II. The maximum left ventricular wall thickness was 22.9 ± 8.7 mm and left ventricular ejection fraction was 53.4 ± 6.6%. Left ventricular hypertrophy was present in 19 individuals (86%) at baseline. 17 patients had an WPW pattern (77%). After a mean follow-up period of 7 years, 2 patients had undergone accessory pathway ablation, 8 patients (36%) underwent permanent pacemaker implantation (atrio-ventricular blocks—5; sinus node disease—2), 3 patients developed atrial fibrillation, 11 patients (50%) developed progressive worsening in NYHA functional class, and 6 patients (27%) experienced sudden cardiac death or equivalent. PRKAG2 cardiomyopathy must be considered in patients with HCM and progressive conduction system disease.

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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 20 publications

References 0 publications

The genetic determinants of language network dysconnectivity in drug-naïve early stage schizophrenia

The genetic determinants of language network dysconnectivity in drug-naïve early stage schizophrenia

Matrilineal analysis of mutations in the DMD gene in a multigenerational South Indian cohort using DMD gene panel sequencing

Phenotypic expression and clinical outcomes in a South Asian PRKAG2 cardiomyopathy cohort

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