Bozeman, MT, United States
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Today, Golden Helix, Inc. announced a multi-year partnership with Sentieon, a company that develops bioinformatics secondary analysis tools to process genomic data.

Chhangawala S.,New York Medical College | Rudy G.,Golden Helix Inc. | Mason C.E.,New York Medical College | Mason C.E.,Rutgers Cancer Institute of New Jersey | And 2 more authors.
Genome Biology | Year: 2015

The initial next-generation sequencing technologies produced reads of 25 or 36 bp, and only from a single-end of the library sequence. Currently, it is possible to reliably produce 300 bp paired-end sequences for RNA expression analysis. While read lengths have consistently increased, people have assumed that longer reads are more informative and that paired-end reads produce better results than single-end reads. We used paired-end 101 bp reads and trimmed them to simulate different read lengths, and also separated the pairs to produce single-end reads. For each read length and paired status, we evaluated differential expression levels between two standard samples and compared the results to those obtained by qPCR. Results: We found that, with the exception of 25 bp reads, there is little difference for the detection of differential expression regardless of the read length. Once single-end reads are at a length of 50 bp, the results do not change substantially for any level up to, and including, 100 bp paired-end. However, splice junction detection significantly improves as the read length increases with 100 bp paired-end showing the best performance. We performed the same analysis on two ENCODE samples and found consistent results confirming that our conclusions have broad application. Conclusions: A researcher could save substantial resources by using 50 bp single-end reads for differential expression analysis instead of using longer reads. However, splicing detection is unquestionably improved by paired-end and longer reads. Therefore, an appropriate read length should be used based on the final goal of the study. © 2015 Chhangawala et al.

Miclaus K.,SAS Institute | Chierici M.,Fondazione Bruno Kessler | Lambert C.,Golden Helix Inc. | Zhang L.,Center for Drug Evaluation and Research | And 6 more authors.
Pharmacogenomics Journal | Year: 2010

The Genome-Wide Association Working Group (GWAWG) is part of a large-scale effort by the MicroArray Quality Consortium (MAQC) to assess the quality of genomic experiments, technologies and analyses for genome-wide association studies (GWASs). One of the aims of the working group is to assess the variability of genotype calls within and between different genotype calling algorithms using data for coronary artery disease from the Wellcome Trust Case Control Consortium (WTCCC) and the University of Ottawa Heart Institute. Our results show that the choice of genotyping algorithm (for example, Bayesian robust linear model with Mahalanobis distance classifier (BRLMM), the corrected robust linear model with maximum-likelihood-based distances (CRLMM) and CHIAMO (developed and implemented by the WTCCC)) can introduce marked variability in the results of downstream case-control association analysis for the Affymetrix 500K array. The amount of discordance between results is influenced by how samples are combined and processed through the respective genotype calling algorithm, indicating that systematic genotype errors due to computational batch effects are propagated to the list of single-nucleotide polymorphisms found to be significantly associated with the trait of interest. Further work using HapMap samples shows that inconsistencies between Affymetrix arrays and calling algorithms can lead to genotyping errors that influence downstream analysis. © 2010 Macmillan Publishers Limited. All rights reserved.

Lambert C.G.,Golden Helix Inc. | Black L.J.,Montana State University | Black L.J.,Greer Black Company
Biostatistics | Year: 2012

Many public and private genome-wide association studies that we have analyzed include flaws in design, with avoidable confounding appearing as a norm rather than the exception. Rather than recognizing flawed research design and addressing that, a category of quality-control statistical methods has arisen to treat only the symptoms. Reflecting more deeply, we examine elements of current genomic research in light of the traditional scientific method and find that hypotheses are often detached from data collection, experimental design, and causal theories. Association studies independent of causal theories, along with multiple testing errors, too often drive health care and public policy decisions. In an era of large-scale biological research, we ask questions about the role of statistical analyses in advancing coherent theories of diseases and their mechanisms. We advocate for reinterpretation of the scientific method in the context of large-scale data analysis opportunities and for renewed appreciation of falsifiable hypotheses, so that we can learn more from our best mistakes. © 2012 The Author.

Golden Helix Inc. | Date: 2012-06-09

Computer software, namely, downloadable software tool for visually exploring genomic data.

Golden Helix Inc. | Date: 2014-07-14

Computer software for managing, analyzing, and visualizing genomic data.

Golden Helix Inc. | Date: 2012-05-24

Computer software for statistical analysis and visualization of data, and user manuals sold therewith.

Golden Helix Inc. | Date: 2010-10-26

Downloadable computer software for managing, analyzing, and visualizing complex genomic data.

PubMed | Golden Helix Inc. and University of California at Los Angeles
Type: | Journal: Molecular psychiatry | Year: 2016

Bipolar disorder (BD) is a common, complex and heritable psychiatric disorder characterized by episodes of severe mood swings. The identification of rare, damaging genomic mutations in families with BD could inform about disease mechanisms and lead to new therapeutic interventions. To determine whether rare, damaging mutations shared identity-by-descent in families with BD could be associated with disease, exome sequencing was performed in multigenerational families of the NIMH BD Family Study followed by in silico functional prediction. Disease association and disease specificity was determined using 5090 exomes from the Sweden-Schizophrenia (SZ) Population-Based Case-Control Exome Sequencing study. We identified 14 rare and likely deleterious mutations in 14 genes that were shared identity-by-descent among affected family members. The variants were associated with BD (P<0.05 after Bonferronis correction) and disease specificity was supported by the absence of the mutations in patients with SZ. In addition, we found rare, functional mutations in known causal genes for neuropsychiatric disorders including holoprosencephaly and epilepsy. Our results demonstrate that exome sequencing in multigenerational families with BD is effective in identifying rare genomic variants of potential clinical relevance and also disease modifiers related to coexisting medical conditions. Replication of our results and experimental validation are required before disease causation could be assumed.Molecular Psychiatry advance online publication, 11 October 2016; doi:10.1038/mp.2016.181.

PubMed | Golden Helix Inc., University of Pennsylvania, University of Texas Medical Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development and 4 more.
Type: Journal Article | Journal: American journal of obstetrics and gynecology | Year: 2015

We sought to use an innovative tool that is based on common biologic pathways to identify specific phenotypes among women with spontaneous preterm birth (SPTB) to enhance investigators ability to identify and to highlight common mechanisms and underlying genetic factors that are responsible for SPTB.We performed a secondary analysis of a prospective case-control multicenter study of SPTB. All cases delivered a preterm singleton at SPTB 34.0 weeks gestation. Each woman was assessed for the presence of underlying SPTB causes. A hierarchic cluster analysis was used to identify groups of women with homogeneous phenotypic profiles. One of the phenotypic clusters was selected for candidate gene association analysis with the use of VEGAS software.One thousand twenty-eight women with SPTB were assigned phenotypes. Hierarchic clustering of the phenotypes revealed 5 major clusters. Cluster 1 (n = 445) was characterized by maternal stress; cluster 2 (n = 294) was characterized by premature membrane rupture; cluster 3 (n = 120) was characterized by familial factors, and cluster 4 (n = 63) was characterized by maternal comorbidities. Cluster 5 (n = 106) was multifactorial and characterized by infection (INF), decidual hemorrhage (DH), and placental dysfunction (PD). These 3 phenotypes were correlated highly by (2) analysis (PD and DH, P < 2.2e-6; PD and INF, P = 6.2e-10; INF and DH, (P = .0036). Gene-based testing identified the INS (insulin) gene as significantly associated with cluster 3 of SPTB.We identified 5 major clusters of SPTB based on a phenotype tool and hierarch clustering. There was significant correlation between several of the phenotypes. The INS gene was associated with familial factors that were underlying SPTB.

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