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      Cardiac Genetic Investigation of Sudden Infant and Early Childhood Death: A Study From Victims to Families

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          Abstract

          Background

          Sudden infant death syndrome (SIDS) is the leading cause of death up to age 1. Sudden unexplained death in childhood (SUDC) is similar but affects mostly toddlers aged 1 to 4. SUDC is rarer than SIDS, and although cardiogenetic testing (molecular autopsy) identifies an underlying cause in a fraction of SIDS, less is known about SUDC.

          Methods and Results

          Seventy‐seven SIDS and 16 SUDC cases underwent molecular autopsy with 25 definitive‐evidence arrhythmia‐associated genes. In 18 cases, another 76 genes with varying degrees of evidence were analyzed. Parents were offered cascade screening. Double‐blind review of clinical‐genetic data established genotype–phenotype correlations. The yield of likely pathogenic variants in the 25 genes was higher in SUDC than in SIDS (18.8% [3/16] versus 2.6% [2/77], respectively; P=0.03), whereas novel/ultra‐rare variants of uncertain significance were comparably represented. Rare variants of uncertain significance and likely benign variants were found only in SIDS. In cases with expanded analyses, likely pathogenic/likely benign variants stemmed only from definitive‐evidence genes, whereas all other genes contributed only variants of uncertain significance. Among 24 parents screened, variant status and phenotype largely agreed, and 3 cases positively correlated for cardiac channelopathies. Genotype–phenotype correlations significantly aided variant adjudication.

          Conclusions

          Genetic yield is higher in SUDC than in SIDS although, in both, it is contributed only by definitive‐evidence genes. SIDS/SUDC cascade family screening facilitates establishment or dismissal of a diagnosis through definitive variant adjudication indicating that anonymity is no longer justifiable. Channelopathies may underlie a relevant fraction of SUDC. Binary classifications of genetic causality (pathogenic versus benign) could not always be adequate.

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          Most cited references81

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            The Sequence Alignment/Map format and SAMtools

            Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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              Fast and accurate short read alignment with Burrows–Wheeler transform

              Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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                Author and article information

                Contributors
                peter.schwartz@unipv.it , p.schwartz@auxologico.it
                Journal
                J Am Heart Assoc
                J Am Heart Assoc
                10.1002/(ISSN)2047-9980
                JAH3
                ahaoa
                Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease
                John Wiley and Sons Inc. (Hoboken )
                2047-9980
                17 August 2023
                05 September 2023
                : 12
                : 17 ( doiID: 10.1002/jah3.v12.17 )
                : e029100
                Affiliations
                [ 1 ] Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics IRCCS Istituto Auxologico Italiano Milan Italy
                [ 2 ] Department of Clinical Genetics Sheffield Children’s NHS Foundation Trust Sheffield United Kingdom
                [ 3 ] Department of Histopathology Sheffield Children’s NHS Foundation Trust Sheffield United Kingdom
                [ 4 ] Sheffield Children’s Hospital NHS Foundation Trust Sheffield United Kingdom
                [ 5 ] Department of Neurosciences University of Sheffield Sheffield United Kingdom
                [ 6 ] Cardiothoracic Centre Northern General Hospital, Sheffield Teaching Hospitals NHS Trust Sheffield United Kingdom
                [ 7 ] Cellular Pathology Department Birmingham Women’s and Children’s Hospital Birmingham United Kingdom
                [ 8 ] Bioinformatics and Statistical Genetics Unit IRCCS Istituto Auxologico Italiano Milan Italy
                [ 9 ] Department of Medicine and Surgery University of Milano‐Bicocca Milan Italy
                [ 10 ] Department of Neonatology Sheffield Teaching Hospitals. NHS Trust Sheffield United Kingdom
                Author notes
                [*] [* ]Correspondence to: Peter J. Schwartz, MD, Center for Cardiac Arrhythmias of Genetic Origin, IRCCS Istituto Auxologico Italiano, Via Pier Lombardo 22, 20135 Milan, Italy. Email: peter.schwartz@ 123456unipv.it or Email: p.schwartz@ 123456auxologico.it
                Author information
                https://orcid.org/0000-0001-9629-2172
                https://orcid.org/0000-0001-5534-444X
                https://orcid.org/0000-0002-3818-9051
                https://orcid.org/0000-0001-5585-2276
                https://orcid.org/0000-0001-8739-6527
                https://orcid.org/0000-0003-0367-1048
                Article
                JAH38672 JAHA/2022/029100-T
                10.1161/JAHA.122.029100
                10547337
                37589201
                b306dd78-06f3-4196-ac33-c7cd7f73ff54
                © 2023 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

                History
                : 03 April 2023
                : 27 June 2023
                Page count
                Figures: 2, Tables: 3, Pages: 16, Words: 11008
                Funding
                Funded by: Lullaby Trust , doi 10.13039/100011714;
                Award ID: 262191
                Funded by: Association of Medical Research Charities , doi 10.13039/501100000532;
                Funded by: Leducq Foundation , doi 10.13039/501100001674;
                Award ID: 18CVD05
                Funded by: Italian Ministry of Health
                Categories
                Original Research
                Original Research
                Arrhythmia and Electrophysiology
                Custom metadata
                2.0
                05 September 2023
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.3.3 mode:remove_FC converted:04.09.2023

                Cardiovascular Medicine
                channelopathies,molecular autopsy,sudden infant death syndrome,sudden unexplained death in childhood,sudden cardiac death

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