遗传性息肉病和结直肠癌的长读DNA和RNA测序:隐性内含子变异和多重突变机制。

IF 3.7 2区 医学 Q2 GENETICS & HEREDITY
Angela L Jacobson, Amal AbuRayyan, Suleyman Gulsuner, Haley Slater, Yagiz Anasiz, Sirajummuneer M Ahmad, Ming K Lee, Jessica Mandell, Emily J Rettner, Eric Q Konnick, Colin Pritchard, Mary-Claire King, Tom Walsh, Brian H Shirts
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引用次数: 0

摘要

背景:分子遗传学诊断对遗传性息肉病和结直肠癌的预防和治疗至关重要。导致这些疾病的19个基因是已知的,但许多严重受影响的患者和家庭仍未得到解决。改变这些基因剪接的隐性内含子变异和不完整的隐性易感性特征导致了这些诊断空白。方法:对4例因错配修复蛋白缺乏和/或家族性息肉病的患者进行适应性取样长读DNA测序,针对19个结肠癌基因,并与直接长读RNA全转录组测序配对,多基因小组检测结果为阴性或不确定种系结果。结果:4例患者均获得遗传诊断。每位患者在不同的结肠癌基因中携带一种隐性内含子种系变异。这些变异通过各种机制取消剪接,都导致基因功能的丧失。患者1是杂合的,因为内含子插入到Alu元件的MSH2中,导致转录延伸到受影响的内含子并停止。患者2是杂合的,深层内含子插入到长穿插核元件(LINE)的APC中,产生假外显子和停止子。患者3在MLH3位点为复合杂合,包括导致外显子跳变和停止的隐内含子替换。患者4在MUTYH为复合杂合,包括产生极短内含子的深度内含子缺失和编码关键蛋白质结构域的外显子转录缺失。结论:配对的长读DNA和RNA测序可以通过检测影响癌症易感性的隐性内含子变异来提高诊断率。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Long-read DNA and RNA sequencing for inherited polyposis and colorectal cancer: cryptic intronic variants and multiple mutational mechanisms.

Background: Molecular genetic diagnoses are critical to prevention and treatment of inherited polyposis and colorectal cancer. 19 genes responsible for these conditions are known, but many severely affected patients and families remain unsolved. Cryptic intronic variants that alter splicing of these genes and incomplete characterisation of recessive predisposition contribute to these diagnostic gaps.

Methods: Adaptive sampling long-read DNA sequencing targeted to 19 colon cancer genes, paired with direct long-read RNA whole-transcriptome sequencing, was undertaken for four patients referred for deficiency of mismatch repair proteins and/or familial polyposis, for whom multigene panel testing yielded negative or uncertain germline results.

Results: Genetic diagnoses were obtained for all four patients. Each patient carried a cryptic intronic germline variant in a different colon cancer gene. The variants abrogated splicing by various mechanisms, all leading to loss of gene function. Patient 1 was heterozygous for intronic insertion into MSH2 of an Alu element, leading to extension of transcription into the affected intron and a stop. Patient 2 was heterozygous for deep intronic insertion into APC of a Long Interspersed Nuclear Element (LINE), creating a pseudoexon and a stop. Patient 3 was compound heterozygous at MLH3, including a cryptic intronic substitution leading to exon skipping and a stop. Patient 4 was compound heterozygous at MUTYH, including a deep intronic deletion yielding an extremely short intron and transcriptional loss of an exon encoding a critical protein domain.

Conclusion: Paired long-read DNA and RNA sequencing can enhance diagnostic yield through detection of cryptic intronic variants that impact cancer predisposition.

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来源期刊
Journal of Medical Genetics
Journal of Medical Genetics 医学-遗传学
CiteScore
7.60
自引率
2.50%
发文量
92
审稿时长
4-8 weeks
期刊介绍: Journal of Medical Genetics is a leading international peer-reviewed journal covering original research in human genetics, including reviews of and opinion on the latest developments. Articles cover the molecular basis of human disease including germline cancer genetics, clinical manifestations of genetic disorders, applications of molecular genetics to medical practice and the systematic evaluation of such applications worldwide.
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