Customer Publications Throughout May 2020

         May 29, 2020

Writing this blog post to summarize and highlight our customer’s publications is undoubtedly one of my favorite things to do! The wide variety of topics is always surprising and inspiring, and I am humbled by the efforts of dedicated scientists who are helping to protect and enrich our lives in so many ways. Our SNP & Variation Suite (SVS) software takes center stage with our customers featured in this month’s post. It is the industry’s ‘go-to’ choice for researchers no matter what species they work with and is perfect for the published works below. If you need a software platform to perform complex analyses on genomic and phenotypic data easily and quickly, click on the titles below to explore in detail how SVS can help you achieve your research goals!

Frequency of Pathogenic/Likely Pathogenic Germline Variants in Cancer-related Genes Among Children with Acute Leukemia in Saudi Arabia

A team of researchers in Saudi Arabia utilized SVS software in their investigation to determine the genetic contributors to pediatric acute leukemia cases in their country. The investigation focused on frequency of detrimental germline mutations in cancer-related genes among pediatric cancer patients who come from highly consanguineous populations such as those found in Saudi Arabia. Using a local sample size of 60 patients who were diagnosed with acute leukemia for their pilot study, they performed whole exome sequencing (WES) using SVS for their initial analysis. Then, they integrated their data with the St. Jude Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE) data portal for curating and classifying germline variants. This allowed them to directly compare risk in their subjects to a sample of pediatric patient’s existing data from the US, where consanguinity is extremely rare. The results of their study showed that the frequency of Pathogenic/Likely Pathogenic mutations among children with consanguineous parents was not significantly different when compared to those reporting no consanguinity. The study did however indicate that larger studies using whole genome sequencing (WGS) would be helpful in further exploration of the role genetics plays in childhood cancer in Saudi Arabia. We are looking forward to hearing how SVS can help with the WGS phase of their next study!

Abdulrahman Alsultan & Colleagues, King Saud University / Published in Social Science & Medicine – Pediatric Blood & Cancer

A Genome-wide Association Study for Resistance to the Insect Pest Leptocybe invasa in Eucalyptus grandis Reveals Genomic Regions and Positional Candidate Defence Genes

Leptocybe invasa, also known as the blue gum chalcid wasp or eucalyptus gall wasp, is a highly invasive insect that has spread from the native range of its host plant’s homeland (thought to be Australia) to wherever Eucalyptus has been imported. The pest is now found around the globe and it threatens one of the most important forest crops, both economically and ecologically, in the world. Although there is some evidence that biological control through parasitoids (parasites used in biological pest control strategies) may be effective in controlling the infestation, breeding for resistant plant stock is still considered a key tool in the fight against L invasa. A team of researchers from South Africa set out to discover if the Eucalyptus grandis species harbors any genetic resistance and selectively bred to aid in defending Eucalyptus forests against the pest. SVS software was used for the analysis in their genome wide association study (GWAS) and GenomeBrowse was used to visualize the Manhattan plots for associated SNPs. This study was the first GWAS of a forest tree species to detect regions of the genome associated with resistance to insects in South Africa. The data the team generated identified seven SNP markers and three genomic regions in two separate populations of E. grandis trees related to resistance to the wasp, thus providing some insight into possible genetic defense mechanisms that may mitigate the damage caused by these highly invasive and destructive insects.

Zander Myburg, Marja O’Neill, Sanushka Naidoo & Colleagues, University of Pretoria / Published in Plant & Cell Physiology

Complete Sequence of the 22q11.2 Allele in 1,053 Subjects with 22q11.2 Deletion Syndrome Reveals Modifiers of Conotruncal Heart Defects

A multi-national team of investigators examined the complex genomic landscape of rare congenital, conotruncal type heart defects (CTD). The team examined genetic data from a group of patients known to have a condition often associated with CTD called 22q11.2 deletion syndrome (22q11.2DS). This disorder is caused by the deletion of a small piece of chromosome 22, near the middle of the chromosome in an area designated q11.2. Their goal was to explore the relationship and possible effect of additional genetic modifiers that may exist in other regions, together with 22q11.2DS. For their investigation, they performed a case-controlled association study involving 22q11.2-affected individuals with congenital heart defects (CHDs) or subtypes within CHD, including CTDs, and a control group of subjects with 22q11.2DS but without heart/aortic arch abnormalities. Using WGS methods, the team employed SVS software’s Multidimensional Outlier Detection method in their Principal Component Analysis. The resulting data, when considered alongside data previously generated in studies using a mouse model, seem to indicate the CRKL gene is the most likely candidate gene to influence risk for CTD’s when combined with 22q11.2DS.

Laura Mitchel, A.J. Agopian & Colleagues, University of Texas Health Sciences Center / Published in The Journal of Human Genetics

Accurate Genomic Predictions for Chronic Wasting Disease in U.S. White-tailed Deer

For those who have grown up with a fondness for wildlife and/or a strong hunting tradition passed down for generations, nothing strikes fear in their hearts like hearing the words “Chronic Wasting Disease”, or CWD as it is commonly referred to. First observed in captive deer herds, this always fatal disease has spread to free-ranging herds of many species of deer, elk, moose and reindeer all over the world. CWD is a transmissible spongiform encephalopathy, which is a family of diseases caused by misfolded proteins called prions. Prion diseases better known to most are bovine spongiform encephalopathy (Mad Cow disease) in cattle, Creutzfeldt-Jakob disease in humans and scrapie in sheep. It is currently unknown if CWD can be transmitted to humans who consume or come in contact with infected animals, but the Center for Disease Control and Prevention has issued precautions for hunters regarding consumption of infected game. Current best management practices have failed to prevent the spread of the disease to game herds in new geographical areas. In search of a novel strategy to reduce the prevalence of CWD, a team of researchers from the US assessed differential susceptibility to the disease using next-generation sequencing. SVS software was used for several steps in their GWA analysis aimed at developing a genomically-estimated CWD eradication program. Their data demonstrated that susceptibility to CWD and variation in natural disease progression are heritable, polygenic traits in the studied population of white-tailed deer. It also supported the use of genome-wide SNP data to produce accurate genomic predictions for risk, thus providing the first novel strategy for reducing the prevalence of CWD through genetic risk assessment in farmed game animals.

Chris Seabury & Colleagues, Texas A & M / Published in G3: Genes, Genomes, Genetics

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