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State-of-the-Art Molecular Genetics in Japan

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Dear colleagues,

This Special Issue of the International Journal of Molecular Sciences (IJMS) aims to rapidly publish contributions on all aspects of molecular genetics and genomes relating to all aspects of life from Japan. We encourage the submission of manuscripts that provide novel and mechanistic insights and papers that report significant advances in the field. Species including but not limited to mammals, rodents, fish, flies, worms, yeast, or other models of disease are of interest. Topics include, but are not limited to, the following:

Gene regulation, chromatin, and epigenetics;
Genome integrity, repair, and replication;
Microbial genetics;
Plant genetic and genomic studies;
Sex differences;
Genes or genomes related to phenotypes and human physiopathology;
Cancer genetics and epigenetics;
Pharmacogenetics and pharmacogenomics;
Toxicogenomics, nutrigenomics, neurogenomics, etc.;
Technological and analytical developments regarding genomic data;
Functional genomics.

Dr. Naoyuki Kataoka
Prof. Dr. Satoshi Kishigami
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Research

16 pages, 1432 KiB

Open AccessArticle

Candidate Genes in Testing Strategies for Linkage Analysis and Bioinformatic Sorting of Whole Genome Sequencing Data in Three Small Japanese Families with Idiopathic Superior Oblique Muscle Palsy

by Toshihiko Matsuo, Chaomulige, Mary Miyaji, Osamu Hosoya, Akira Saito and Kazuyuki Nakazono

Int. J. Mol. Sci. 2022, 23(15), 8626; https://doi.org/10.3390/ijms23158626 - 3 Aug 2022

Cited by 3 | Viewed by 1693

Abstract

Idiopathic superior oblique muscle palsy is a major type of paralytic, non-comitant strabismus and presents vertical and cyclo-torsional deviation of one eye against the other eye, with a large vertical fusion range and abnormal head posture such as head tilt. Genetic background is considered to play a role in its development, as patients with idiopathic superior oblique muscle palsy have varying degrees of muscle hypoplasia and, rarely, the complete absence of the muscle, that is, aplasia. In this study, whole genome sequencing was performed, and single nucleotide variations and short insertions/deletions (SNVs/InDels) were annotated in two patients each in three small families (six patients in total) with idiopathic superior oblique muscle palsy, in addition to three normal individuals in one family. At first, linkage analysis was carried out in the three families and SNVs/InDels in chromosomal loci with negative LOD scores were excluded. Next, SNVs/InDels shared by the six patients, but not by the three normal individuals, were chosen. SNVs/InDels were further narrowed down by choosing low-frequency (<1%) or non-registered SNVs/InDels in four databases for the Japanese population, and then by choosing SNVs/InDels with functional influence, leading to one candidate gene, SSTR5-AS1 in chromosome 16. The six patients were heterozygous for 13-nucleotide deletion in SSTR5-AS1, except for one homozygous patient, while the three normal individuals were wild type. Targeted polymerase chain reaction (PCR) and direct sequencing of PCR products confirmed the 13-nucleotide deletion in SSTR5-AS1. In the face of newly-registered SSTR5-AS1 13-nucleotide deletion at a higher frequency in a latest released database for the Japanese population, the skipping of low-frequency and non-registration sorting still resulted in only 13 candidate genes including SSTR5-AS1 as common variants. The skipping of linkage analysis also led to the same set of 13 candidate genes. Different testing strategies that consisted of linkage analysis and simple unintentional bioinformatics could reach candidate genes in three small families with idiopathic superior oblique muscle palsy. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics in Japan)

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