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A 12-kb structural variation in progressive myoclonic epilepsy was newly identified by long-read whole-genome sequencing.

Abstract：

:We report a family with progressive myoclonic epilepsy who underwent whole-exome sequencing but was negative for pathogenic variants. Similar clinical courses of a devastating neurodegenerative phenotype of two affected siblings were highly suggestive of a genetic etiology, which indicates that the survey of genetic variation by whole-exome sequencing was not comprehensive. To investigate the presence of a variant that remained unrecognized by standard genetic testing, PacBio long-read sequencing was performed. Structural variant (SV) detection using low-coverage (6×) whole-genome sequencing called 17,165 SVs (7,216 deletions and 9,949 insertions). Our SV selection narrowed down potential candidates to only five SVs (two deletions and three insertions) on the genes tagged with autosomal recessive phenotypes. Among them, a 12.4-kb deletion involving the CLN6 gene was the top candidate because its homozygous abnormalities cause neuronal ceroid lipofuscinosis. This deletion included the initiation codon and was found in a GC-rich region containing multiple repetitive elements. These results indicate the presence of a causal variant in a difficult-to-sequence region and suggest that such variants that remain enigmatic after the application of current whole-exome sequencing technology could be uncovered by unbiased application of long-read whole-genome sequencing.

journal_name

J Hum Genet

journal_title

Journal of human genetics

authors

Mizuguchi T,Suzuki T,Abe C,Umemura A,Tokunaga K,Kawai Y,Nakamura M,Nagasaki M,Kinoshita K,Okamura Y,Miyatake S,Miyake N,Matsumoto N

doi

10.1038/s10038-019-0569-5

subject

Has Abstract

pub_date

2019-05-01 00:00:00

pages

359-368

issue

5

eissn

1434-5161

issn

1435-232X

pii

10.1038/s10038-019-0569-5

journal_volume

64

pub_type

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