Our recent Variant Analysis update includes several key features, most notably, improved data export (now completed offline to improve performance) and better handling of uploaded VCF files. The Allele Frequency Community (AFC) now features CentoMD data, with details about 155,000 sequenced individuals whose genotypes offer a more comprehensive view of population genomics. We also updated the statistics available in AFC, which contains summary statistics from public, private and users from QIAGEN’s community. These statistics are now based on more than 750,000 samples that were analyzed through our platforms—including more than 38,000 whole genomes, and more than 358,000 exome samples. The new Variant Analysis release inspired us to look at how our customers are putting it to use it in their workflows. Read on for more details—and possibly some inspiration!
Oligogenic genetic variation of neurodegenerative disease genes in 980 postmortem human brains
First author: Michael J. Keogh
The Journal of Neurology, Neurosurgery and Psychiatry recently published a study developed by an UK-based team that analyzed genetic variants of three neurodegenerative diseases in 980 postmortem human brains. They used Variant Analysis to study 49 genes known to be associated with three neurodegenerative disorders: Alzheimer’s disease (AD), Parkinson’s disease-dementia with Lewy bodies (PD-DLB), and frontotemporal dementia-amyotrophic lateral sclerosis (FTD-ALS), and investigated whether synergistic interaction between two or more functional genetic variants contributed to increased likelihood of early onset. They determined that the presence of oligogenic variants did not influence the age of onset or disease severity, which they noted is an important a priori bias to guard against in future research.
Mutational landscape of radiation-associated angiosarcoma of the breast
First author: Bryan J. Thibodeau
A team of scientists from Michigan, California, and Alberta, Canada recently investigated genomic variation in biospecimens from radiation-associated breast angiosarcomas—a rare complication of radiation therapy for breast carcinoma. In their report, which was published in Oncotarget, the team mentioned using Variant Analysis to characterize variants and to investigate signaling pathways preferentially affected in radiation-association angiosarcomas. Due to the relative rarity of this type of tumor, the team recommended further investigation, using whole genome or exome sequencing, to further the discovery and confirmation of potential drug targets and to identify potential radiation-associated signatures.
Pediatric dilated cardiomyopathy‐associated LRRC10 (Leucine‐Rich Repeat–Containing 10) variant reveals LRRC10 as an auxiliary subunit of cardiac L‐type Ca2+ channels
First Author: Marites T. Woon
A group of researchers from Madison, Wisc., and Rochester, Minn. sought to further understand the genetic causes of dilated cardiomyopathy (DCM). Their report, published in the Journal of the American Heart Association, details their work and includes mention of Variant Analysis to analyze variant call format files. The team found a rare, homozygous variant in a cardiac‐specific protein, which provides evidence that variants in LRRC10 can serve as a genetic cause of DCM. This research deepens our burgeoning understanding of the condition and provides a potential link to its pathophysiology.
ARL6IP1 mutation causes congenital insensitivity to pain, acromutilation and spastic paraplegia
First Author: M. Nizon
A team from Nantes, France, reported in Clinical Genetics about their research on the role of ARL6IP1 in the pathophysiology of insensitivity to pain and spastic paraplegia, which are symptoms of hereditary sensory and autonomic neuropathies (HSAN) type II. They used Variant Analysis to generate variant annotation and interpretation analyses, enabling them to identify a homozygous variant in ARL6IP1, which they determined as a key factor in hereditary spastic paraplegia and sensorimotor neuropathy.
We’re not only honored to understand how our solutions are helping a range of researchers learn more about their fields, we’re also keen to learn more. If you’d like your work to be featured in one of our blog posts, we’d love to hear from you. To test out Variant Analysis for yourself, simply request it here.
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