RT Journal Article
SR Electronic
T1 A targeted sequencing extension for transcript genotyping in single-cell transcriptomics
JF Life Science Alliance
JO Life Sci. Alliance
FD Life Science Alliance LLC
SP e202301971
DO 10.26508/lsa.202301971
VO 6
IS 11
A1 Van Horebeek, Lies
A1 David, Margaux
A1 Dedoncker, Nina
A1 Mallants, Klara
A1 Bijnens, Baukje
A1 Goris, An
A1 Dubois, Bénédicte
YR 2023
UL http://www.life-science-alliance.org/content/6/11/e202301971.abstract
AB As no existing methods within the single-cell RNA sequencing repertoire combine genotyping of specific genomic loci with high throughput, we evaluated a straightforward, targeted sequencing approach as an extension to high-throughput droplet-based single-cell RNA sequencing. Overlaying standard gene expression data with transcript level genotype information provides a strategy to study the impact of genetic variants. Here, we describe this targeted sequencing extension, explain how to process the data and evaluate how technical parameters such as amount of input cDNA, number of amplification rounds, and sequencing depth influence the number of transcripts detected. Finally, we demonstrate how targeted sequencing can be used in two contexts: (1) simultaneous investigation of the presence of a somatic variant and its potential impact on the transcriptome of affected cells and (2) evaluation of allele-specific expression of a germline variant in ad hoc cell subsets. Through these and other comparable applications, our targeted sequencing extension has the potential to improve our understanding of functional effects caused by genetic variation.