Diagnosis of late-onset Pompe disease and other muscle disorders by next-generation sequencing

Orphanet Journal of Rare Diseases
Sébastien LévesquePriya Kishnani

Abstract

Late-onset Pompe disease (LOPD) is a rare treatable lysosomal storage disorder characterized by progressive lysosomal glycogen accumulation and muscle weakness, with often a limb-girdle pattern. Despite published guidelines, testing for LOPD is often overlooked or delayed in adults, owing to its low frequency compared to other muscle disorders with similar muscle patterns. Next-generation sequencing has the capability to test concurrently for several muscle disorders. This could potentially lead to increased diagnosis of LOPD, disorders with non-specific muscle weakness or atypical patients. We developed a gene panel to further study its clinical utility in a cohort of patients with suspected muscle disorders. We designed a gene panel to analyze the coding sequences and splice site junctions of GAA causing LOPD, along with 77 other genes causing muscle disorders with overlapping phenotypes. At a median coverage of ~200X (sequences per base), all GAA exons were successfully covered with >20X and only 0.3 % of exons across all genes were <20X. The panel showed an excellent sensitivity (100 %) and specificity (98 %) across all selected genes, using known variations in Pompe patients and controls. We determined its clinical utility...Continue Reading

References

Jul 17, 1999·Neuromuscular Disorders : NMD·E M HoogerwaardM de Visser
Sep 14, 1999·European Journal of Human Genetics : EJHG·M G AusemsA T van der Ploeg
May 17, 2006·Genetics in Medicine : Official Journal of the American College of Medical Genetics·UNKNOWN ACMG Work Group on Management of Pompe DiseaseMichael S Watson
May 17, 2006·Genetics in Medicine : Official Journal of the American College of Medical Genetics·R Rodney HowellAns van der Ploeg
May 17, 2006·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Rhona M JackDeeksha Bali
Jun 2, 2006·The Journal of Pediatrics·Priya S KishnaniUNKNOWN Infantile-Onset Pompe Disease Natural History Study Group
May 26, 2007·Brain : a Journal of Neurology·Carina Wallgren-PetterssonBjarne Udd
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Oct 7, 2009·Neurology·N B RomeroC Wallgren-Pettersson
Dec 10, 2009·Nature Reviews. Genetics·Michael L Metzker
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
Oct 1, 2011·Genome Biology·Anna-Maija SulonenJanna Saarela
Jan 19, 2012·American Journal of Medical Genetics. Part C, Seminars in Medical Genetics·Angela SchüllerBenedikt Schoser
Jan 19, 2012·American Journal of Medical Genetics. Part C, Seminars in Medical Genetics·Priya S KishnaniNancy J Mendelsohn
Jan 19, 2012·American Journal of Medical Genetics. Part C, Seminars in Medical Genetics·Barbara K Burton
Jan 19, 2012·American Journal of Medical Genetics. Part C, Seminars in Medical Genetics·Marian KroosArnold J J Reuser
Feb 1, 2012·Journal of Inherited Metabolic Disease·Caroline RegneryBenedikt Schoser
Jun 6, 2012·Molecular Genetics and Metabolism·Lisa D Hobson-WebbPriya S Kishnani
Jan 10, 2013·European Journal of Human Genetics : EJHG·Sandra MercierIsabelle Desguerre
Feb 28, 2013·European Journal of Human Genetics : EJHG·Mariacristina ScotoFrancesco Muntoni
Nov 16, 2013·Nucleic Acids Research·Melissa J LandrumDonna R Maglott
Nov 19, 2013·American Journal of Medical Genetics. Part a·Chia-Feng YangDau-Ming Niu
Feb 12, 2014·Clinica Chimica Acta; International Journal of Clinical Chemistry·Hsuan-Chieh LiaoYann-Jang Chen
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Jul 20, 2014·Neurologic Clinics·Matthew P Wicklund, John T Kissel
Aug 1, 2014·Pediatric Neurology·Shalea J PiteauJennifer J MacKenzie
Aug 12, 2014·BMC Genomics·Pubudu Saneth SamarakoonRobert Lyle
Oct 19, 2014·JAMA : the Journal of the American Medical Association·Hane LeeStanley F Nelson
Oct 31, 2014·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Kyle RettererEden Haverfield
Nov 8, 2014·Annals of Neurology·Arunkanth AnkalaMadhuri R Hegde
Nov 21, 2014·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Mark B ConsugarEric A Pierce

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Citations

Jun 18, 2016·Neuromuscular Disorders : NMD·Teresinha EvangelistaUNKNOWN VCP related diseases Consortium
Dec 11, 2017·Practical Neurology·James B LillekerMark Roberts
Feb 2, 2018·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Fanny ThuriotSébastien Lévesque
Mar 18, 2019·Journal of Clinical Pathology·Marija MeznaricLea Leonardis
Sep 12, 2019·Molecular Genetics & Genomic Medicine·Fernanda Sperb-LudwigIda Vanessa Doederlein Schwartz
Dec 19, 2016·Frontiers in Molecular Biosciences·Wai Kwan Tang, Di Xia
Apr 28, 2020·Neurology. Genetics·Fanny ThuriotSébastien Lévesque
Aug 23, 2020·Cells·Valentina La CognataSebastiano Cavallaro
May 10, 2018·Arquivos de neuro-psiquiatria·Paulo José LorenzoniRosana Herminia Scola
Sep 17, 2020·Life·Ozlem Goker-AlpanPriya S Kishnani
May 1, 2021·Diagnostics·Andrea BarpValeria Ada Sansone
May 21, 2021·Circulation Journal : Official Journal of the Japanese Circulation Society·Thuy Vy NguyenThuy Duong Ho Huynh
Jun 17, 2021·Muscle & Nerve·Stefan NicolauTeerin Liewluck
Nov 11, 2017·Molecular Genetics and Metabolism·Mari MoriPriya S Kishnani

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Datasets Mentioned

BETA
NA12878

Methods Mentioned

BETA
PCR
biopsy
gene panel
exome sequencing

Software Mentioned

Burrows Aligner
Integrative Genomics Viewer
SAMtools
SnpEff
Genome Analysis Toolkit
Trimmomatic
SnpSift
Galaxy
Picard
haplotypeCaller

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