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Eur J Hum Genet. 2019 Feb 14. doi: 10.1038/s41431-019-0343-3. [Epub ahead of print]

Using dried blood spot samples from a trio for linked-read whole-exome sequencing.

Author information

1
FarGen, The Genetic Biobank of the Faroe Islands, Tórshavn, Faroe Islands.
2
General Medical Department, National Hospital of the Faroe Islands, Tórshavn, Faroe Islands.
3
FarGen, The Genetic Biobank of the Faroe Islands, Tórshavn, Faroe Islands. noomi@fargen.fo.

Abstract

Long-term collection of dried blood spot (DBS) samples through newborn screening may have retrospective and prospective advantages, especially in combination with advanced analytical techniques. This work concerns whether linked-reads may overcome some of the limitations of short-read sequencing of DBS samples, such as performing molecular phasing. We performed whole-exome sequencing of DNA extracted from DBS and corresponding whole blood (WB) reference samples, belonging to a trio with unaffected parents and a proband affected by primary carnitine deficiency (PCD). For the DBS samples we were able to phase >21% of the genes under 100 kb, >40% of the SNPs, and the longest phase block was >72 kb. Corresponding results for the WB reference samples was >85%, >75%, and >915 kb, respectively. Concerning the PCD causing variant (rs72552725:A > G) in the SLC22A5 gene we observe full genotype concordance between DBS and WB for all three samples. Furthermore, we were able to phase all variants within the SLC22A5 gene in the proband's WB data, which shows that linked-read sequencing may replace the trio information for haplotype detection. However, due to smaller molecular lengths in the DBS data only small phase blocks were observed in the proband's DBS sample. Therefore, further optimisation of the DBS workflow is needed in order to explore the full potential of DBS samples as a test bed for molecular phasing.

PMID:
30765883
DOI:
10.1038/s41431-019-0343-3

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