Thermo ebook on eQTL - 31

One change in a DNA's nucleotides can trigger many diseases, from cancer to sickle cell anemia and beyond. Image from Dreamstime.

They developed AmpliSolve, a bioinformatics tool.3
Lise and his colleagues started with germline samples, where the variation is less complicated: 50%
for heterozygous and 100% for homozygous. "We
developed a model that established the locationspecific error in sequencing," Lise explains. The nucleotide composition of an area on a gene impacts
the odds of an error in sequencing with some platforms. For example, some sequencing devices have
trouble distinguishing a stretch of seven G nucleotides, maybe missing one or getting one wrong.

Ultimately, scientists want to understand the biology of SNVs, and clinicians want to use the information to treat diseases. It all goes to show what just a
single change can do-bad and good.

References
1.

Jin, HJ; Jung, S; DebRoy, AR; et al. Identification
and validation of regulatory SNPs that modulate
transcription factor chromatin binding and gene
expression in prostate cancer. Oncotarget 2016.

So, Lise and his colleagues determined the typical
sequencing-error rate for locations on genes, and
AmpliSolve uses that to distinguish an artefact
from an SNV. Say that a location's typical sequencing error rate is 1%, then any variation of 1% or less
is considered artefact, and any variation greater
than 1% is considered real. As Lise explains it, "We
get rid of the artefact, so that we can spot what is a
potential effect."

7(34):54616-54626. [PMID 27409348]
2.

Cannataro, VL; Gaffney, SG; Townsend, JP. Effect sizes of
somatic mutations in cancer. J. Natl. Cancer Inst. 2018.
110(11):1171-1177. [PMID 30365005]

3.

Jayaram, A; Sandhu, S; Wong, SQ; et al. Identification of
single nucleotide variants using position-specific error
estimation in deep sequencing data. bioRxiv. 2018.

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https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+27409348 https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+30365005 https://www.biorxiv.org/content/10.1101/475947v1

Thermo ebook on eQTL

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