Mobile element insertions (MEIs) typically exceed the read lengths of short-read sequencing technologies and are therefore frequently missed. Recently, a founder Alu insertion in exon 4 of RP1 has been detected in Japanese patients with macular dystrophy by PCR and gel electrophoresis. We aimed to develop a grep search program for the detection of the Alu insertion in exon 4 of RP1 using unprocessed short reads. Among 494 unrelated Korean patients with inherited eye diseases, 273 patients with specific retinal phenotypes who were previously genotyped by targeted panel or whole exome sequencing were selected. Five probands had a single heterozygous truncating RP1 variant, and one of their unaffected parents also carry this variant. To find a hidden genetic variant, whole genome sequencing was performed in two patients, and it revealed AluY c.4052_4053ins328/p.(Tyr1352Alafs*9) insertion in RP1 exon 4. This AluY insertion was additionally identified in other 3 families, which was confirmed by PCR and gel electrophoresis. We developed simplified grep search program to detect this AluY insertion in RP1 exon 4. The simple grep search revealed a median variant allele frequency of 0.282 (interquartile range, 0.232-0.383), with no false-positive results using 120 control samples. The MEI in RP1 exon 4 was a common founder mutation in Korean, occurring in 1.8% of our cohort. The RP1-Alu grep program efficiently detected the AluY insertion, without the preprocessing of raw data or complex installation processes.
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http://dx.doi.org/10.1038/s41598-021-92834-4 | DOI Listing |
Neurol Genet
December 2024
From the The Institute of Clinical Medicine (K.Õ., T.R., E.Õ.-S., L.M., S. Pajusalu), Faculty of Medicine, University of Tartu; Genetics and Personalized Medicine Clinic (K.Õ., T.R., L.M., Sander Pajusalu); Children's Clinic (E.O.-S.); Pathology Department (S. Puusepp), Tartu University Hospital, Estonia; Folkhalsan Research Center (M.S., B.U.), Helsinki; and Tampere Neuromuscular Center (B.U.), Tampere, Finland.
Background And Objectives: Tibial muscular dystrophy (TMD) is an autosomal dominant, slowly progressive late-onset distal myopathy. TMD was first described in 1991 by Udd et al. in Finnish patients, who were later found to harbor a heterozygous unique 11-bp insertion/deletion in the last exon of the gene-the Finnish founder variant (FINmaj).
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Department of Molecular & Cellular Biosciences, University of Cincinnati, Cincinnati, OH 45267.
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Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, No. 1, Section 4, Roosevelt Rd., Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, No. 7, Chung-Shan South Road, Zhongzheng Dist., Taipei City 100, Taiwan. Electronic address:
Background: Inadequate tumour samples often hinder molecular testing in non-small cell lung cancer (NSCLC). Plasma-based cell-free DNA (cfDNA) sequencing has shown promise in bypassing these tissue limitations. Nevertheless, pleural effusion (PE) samples may offer a richer cfDNA source for mutation detection in patients with malignant PE.
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Department of Pathology and Applied Neurobiology, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, 465 Kajii-Cho, Kawaramachi Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan.
Duchenne/Becker muscular dystrophy (DMD/BMD) manifests progressive muscular dystrophy and non-progressive central nervous disorder. The neural disorder is possibly caused by abnormalities in the developmental period; however, basic research to understand the mechanisms remains underdeveloped. The responsible gene, Dmd (dystrophin), generates multiple products derived from several gene promoters.
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