Customer Publications Throughout September 2019

From diagnosing, treating and preventing diseases in humans and animals, to preserving our global food supply, Golden Helix products are being used all over the world! In September, we were cited in many publications spanning a diverse range of species and topics. Below are brief recaps of a few of the studies where SNP & Variation Suite (SVS) and VarSeq have been cited. To read each study in its entirety, click on the title and it will take you to the publication. Perhaps you will be inspired to use Golden Helix software in a new and innovative way by some of the important discoveries outlined below!

Rectal Cancer Sub-clones Respond Differentially to Neoadjuvant Therapy

A collaborative team from the University of Michigan and the University of Alabama investigated the effect of sub-clones within colorectal cancer tumors. With the help of VarSeq to perform whole-exome sequencing on multiple pre and post-treatment tumor samples, the team was able to produce data which sheds some light on how these sub-clones can effect neoadjuvant chemoradiotherapy (nCRT) treatment response. Recognizing that each tumor may have several unique modes of activity indicates a more comprehensive genomic analysis would be beneficial for determining therapeutic resistance to treatments for rectal cancer. This first of its kind study will pave the way for further investigations in the fight against colorectal cancer.

Peter Ulintz & Colleagues, University of Michigan / Published in Science Direct – Neoplasia 

Predictive Value of Genomic Screening: Cross-sectional Study of Cystic Fibrosis in 50,788 Electronic Health Records

As the role of Electronic Health Records (EHR) becomes more influential and sophisticated, so does their use as a diagnostic tool. Is it possible to diagnose certain diseases by accessing the electronic data of previously diagnosed patients? One team led by investigators from Geisinger Health set out to prove that EHR-focused examination of genomic screening has value in the case of Cystic Fibrosis (CF) diagnosis. Using SVS software in their whole-exome sequencing methods, the team demonstrated how useful and predictive a genome-first screening of EHR’s can be. As more and more health care systems embrace and utilize the automation of patient records, it is a safe bet that we will hear more in the future regarding the predictive value of analyzing genomic screening date gleaned from EHR’s.

Lin Mirshahi & Colleagues, Geisinger Health System / Published in Nature – npj Genomic Medicine

Partial LPL Deletions: Rare Copy-Number Variants Contributing Towards the Polygenic Form of Severe Hypertriglyceridemia

Using VarSeq’s CNV tool, VS-CNV, an international group studied the role of Copy-Number Variants (CNV) in patients with severe hypertriglyceridemia (HTG). The team, which included members from the Robarts Research Institute in Canada, demonstrated how recent improvements in next-generation sequencing (NGS) and bioinformatic analyses allowed them to identify novel CNV deletions in the LPL gene of patients with severe HTG. The data suggests that a greater understanding of the genetic factors contributing to HTG can be found by incorporating the new suite of NGS diagnostic tools available to the health care community, which will ultimately enhance precision medicine.

John Robinson, Jian Wang & Colleagues, Robarts Research Institute / Published in the Journal of Lipid Research

Additional Evidence for DDB2 T338M as a Genetic Risk Factor for Ocular Squamous Cell Carcinoma in Horses

Veterinary researchers from the University of California, Davis and around the US explored the link between a missense mutation in damage-specific DNA-binding protein 2 (DDB2 T338M) and periocular cancer in horses. Building on previously published research which utilized SVS software to determine the role of DDB2 T3338M in the occurrence of ocular squamous cell carcinoma (SCC) in Haflinger and Belgian horse breeds, the team again used SVS for their statistical analysis (association testing) to determine if this mutation also contributes to the risk of ocular SCC in Arabian, Appaloosa and Percheron breeds. Ocular SCC is the second most common tumor affecting the equine eye and is widely known to be associated with UV damage. There is strong evidence this mutation is hindering the body’s ability to repair UV-damaged DNA. The data supports using genetic testing to screen horses for this variant in order to aid with clinical management of cases and to enable breeders to make sound breeding decisions. Many have already implemented this approach in their breeding programs.

Rebecca R. Bellone & Colleagues, University of California, Davis / Published in the International Journal of Genomics

Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces

Biodiversity in plants used for food and agriculture is instrumental in sustaining ecosystem operations, the resilience of the plants and productivity of crops. Researchers in Italy recently utilized SVS software to filter the single nucleotide polymorphisms (SNPs) of 50 common bean landraces grown in Italy to assess population genetics and phylogenetic relationships. Although there are two distinct and known gene pools of the common beans cultivated worldwide today, the local populations grown in marginal areas are especially adapted to the environment of the cultivation area as well as the uses and cultures of the farmers who grow them. The authors are hoping the knowledge gained and methods used will help preserve specialized landraces from genetic erosion and ultimately extinction, thus supporting the agrobiodiversity of this important nutritional crop.

Stefano Pavan & Colleagues, University of Bari / Published in Diversity

GWAS Identifies Genetic Variants Associated with Omega-3 Fatty Acid Composition of Atlantic Salmon Fillets

Norwegian scientists used SVS software in a genome-wide association study with the goal of identifying genetic variants associated with long-chain omega-3 fatty acid content in the muscle of Atlantic salmon. Building on their previous investigations, the group is striving to understand the decrease of omega-3 long-chain polyunsaturated fatty acids which has been increasingly exhibited over decades of farming this important food source. If successful, the data could be used to selectively breed Atlantic salmon that would boost the beneficial fatty acid content of farmed fish. Although this analysis method has been used to identify the genes responsible for the fatty acid content in the meat of cattle and pigs, fish have a complex genetic architecture which makes the team’s work challenging. This study is likely to be just one piece of a very large puzzle and I look forward to seeing where subsequent investigations will lead them!

Hooman Moghadam, Borghild Hillestad & Colleagues, SalmoBreed AS / Published in Aquaculture

To access the complete list of publications citing Golden Helix products, please visit our Published Articles page on our website.

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