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Novel pathogenic variants and genes for myopathies identified by whole exome sequencing.

Hunter JM, Ahearn ME, Balak CD, Liang WS, Kurdoglu A, Corneveaux JJ, Russell M, Huentelman MJ, Craig DW, Carpten J, Coons SW, DeMello DE, Hall JG, Bernes SM, Baumbach-Reardon L - Mol Genet Genomic Med (2015)

Bottom Line: Neuromuscular diseases (NMD) account for a significant proportion of infant and childhood mortality and devastating chronic disease.Determining the specific diagnosis of NMD is challenging due to thousands of unique or rare genetic variants that result in overlapping phenotypes.Our results demonstrate the utility and genetic diagnostic value of WES in the broad class of NMD phenotypes.

View Article: PubMed Central - PubMed

Affiliation: Integrated Cancer Genomics, Translational Genomics Research Institute (TGen) Phoenix, Arizona.

ABSTRACT
Neuromuscular diseases (NMD) account for a significant proportion of infant and childhood mortality and devastating chronic disease. Determining the specific diagnosis of NMD is challenging due to thousands of unique or rare genetic variants that result in overlapping phenotypes. We present four unique childhood myopathy cases characterized by relatively mild muscle weakness, slowly progressing course, mildly elevated creatine phosphokinase (CPK), and contractures. We also present two additional cases characterized by severe prenatal/neonatal myopathy. Prior extensive genetic testing and histology of these cases did not reveal the genetic etiology of disease. Here, we applied whole exome sequencing (WES) and bioinformatics to identify likely causal pathogenic variants in each pedigree. In two cases, we identified novel pathogenic variants in COL6A3. In a third case, we identified novel likely pathogenic variants in COL6A6 and COL6A3. We identified a novel splice variant in EMD in a fourth case. Finally, we classify two cases as calcium channelopathies with identification of novel pathogenic variants in RYR1 and CACNA1S. These are the first cases of myopathies reported to be caused by variants in COL6A6 and CACNA1S. Our results demonstrate the utility and genetic diagnostic value of WES in the broad class of NMD phenotypes.

No MeSH data available.


Related in: MedlinePlus

Histopathology images of frozen muscle biopsy cross sections from the affected male child in F038 carrying a homozygous p.Lys2483Glu COL6A3 pathogenic variant. (A) H&E stain reveals atrophic (arrowheads), hypertrophic (stars), and split fibers (arrows). Also present are internal nuclei and connective tissue proliferation. Magnification = 100×. (B) ATPase reaction stain at pH 4.6 demonstrating that both fiber types are affected by hypertrophy and atrophy as well as mild fiber type grouping. Magnification = 100×. (C) NADH oxidative enzyme reaction stain demonstrating myofibrillar architectural disarray (moth-eaten fibers). Magnification = 400×.
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fig01: Histopathology images of frozen muscle biopsy cross sections from the affected male child in F038 carrying a homozygous p.Lys2483Glu COL6A3 pathogenic variant. (A) H&E stain reveals atrophic (arrowheads), hypertrophic (stars), and split fibers (arrows). Also present are internal nuclei and connective tissue proliferation. Magnification = 100×. (B) ATPase reaction stain at pH 4.6 demonstrating that both fiber types are affected by hypertrophy and atrophy as well as mild fiber type grouping. Magnification = 100×. (C) NADH oxidative enzyme reaction stain demonstrating myofibrillar architectural disarray (moth-eaten fibers). Magnification = 400×.

Mentions: In Family 38, a male child of Canadian descent was born at term with club feet but no additional problems (Table1). He walked somewhat late and since has had a consistently mild abnormal gait. At the age of 5–6 years, he underwent a period of weight loss and lipoatrophy, and at age 17 had a body mass index (BMI) in the first centile, and continued to have a malnourished appearance and difficulty gaining weight. From the age of 8 to age 17, he complained of significant weakness and fatigue. He displayed mild progressive proximal thoracic scoliosis and had significant but nonfixed bilateral lower extremity contractures of hamstrings, ankles, and feet with overlapping toes (Table1). He had no history of skin rash. His respiration and cardiac function were normal. Testing revealed a consistent mild elevation of CPK. Electromyography (EMG) suggested chronic motor neuropathy. Abnormalities revealed by muscle biopsy histology included size variation, split fibers, internal nuclei, connective tissue proliferation, and endomysium proliferation (Fig.1A). ATPase staining revealed moderate Type I and Type II grouping (Fig.1B). NADH staining revealed moth-eaten fibers (Fig.1C). The overall histological diagnosis was abnormal myofibrillar architecture with moderate fiber type grouping of unknown etiology. Genetic sequencing of 15 NMD genes was normal (Table1). Over his 17 years of life, his diagnoses included Charcot–Marie–Tooth disease, myopathy, Pompe disease, MD, limb-girdle muscular dystrophy (LGMD), and spinal muscular atrophy, but without genetic confirmation. There is no other known history of NMD in the family.


Novel pathogenic variants and genes for myopathies identified by whole exome sequencing.

Hunter JM, Ahearn ME, Balak CD, Liang WS, Kurdoglu A, Corneveaux JJ, Russell M, Huentelman MJ, Craig DW, Carpten J, Coons SW, DeMello DE, Hall JG, Bernes SM, Baumbach-Reardon L - Mol Genet Genomic Med (2015)

Histopathology images of frozen muscle biopsy cross sections from the affected male child in F038 carrying a homozygous p.Lys2483Glu COL6A3 pathogenic variant. (A) H&E stain reveals atrophic (arrowheads), hypertrophic (stars), and split fibers (arrows). Also present are internal nuclei and connective tissue proliferation. Magnification = 100×. (B) ATPase reaction stain at pH 4.6 demonstrating that both fiber types are affected by hypertrophy and atrophy as well as mild fiber type grouping. Magnification = 100×. (C) NADH oxidative enzyme reaction stain demonstrating myofibrillar architectural disarray (moth-eaten fibers). Magnification = 400×.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4521965&req=5

fig01: Histopathology images of frozen muscle biopsy cross sections from the affected male child in F038 carrying a homozygous p.Lys2483Glu COL6A3 pathogenic variant. (A) H&E stain reveals atrophic (arrowheads), hypertrophic (stars), and split fibers (arrows). Also present are internal nuclei and connective tissue proliferation. Magnification = 100×. (B) ATPase reaction stain at pH 4.6 demonstrating that both fiber types are affected by hypertrophy and atrophy as well as mild fiber type grouping. Magnification = 100×. (C) NADH oxidative enzyme reaction stain demonstrating myofibrillar architectural disarray (moth-eaten fibers). Magnification = 400×.
Mentions: In Family 38, a male child of Canadian descent was born at term with club feet but no additional problems (Table1). He walked somewhat late and since has had a consistently mild abnormal gait. At the age of 5–6 years, he underwent a period of weight loss and lipoatrophy, and at age 17 had a body mass index (BMI) in the first centile, and continued to have a malnourished appearance and difficulty gaining weight. From the age of 8 to age 17, he complained of significant weakness and fatigue. He displayed mild progressive proximal thoracic scoliosis and had significant but nonfixed bilateral lower extremity contractures of hamstrings, ankles, and feet with overlapping toes (Table1). He had no history of skin rash. His respiration and cardiac function were normal. Testing revealed a consistent mild elevation of CPK. Electromyography (EMG) suggested chronic motor neuropathy. Abnormalities revealed by muscle biopsy histology included size variation, split fibers, internal nuclei, connective tissue proliferation, and endomysium proliferation (Fig.1A). ATPase staining revealed moderate Type I and Type II grouping (Fig.1B). NADH staining revealed moth-eaten fibers (Fig.1C). The overall histological diagnosis was abnormal myofibrillar architecture with moderate fiber type grouping of unknown etiology. Genetic sequencing of 15 NMD genes was normal (Table1). Over his 17 years of life, his diagnoses included Charcot–Marie–Tooth disease, myopathy, Pompe disease, MD, limb-girdle muscular dystrophy (LGMD), and spinal muscular atrophy, but without genetic confirmation. There is no other known history of NMD in the family.

Bottom Line: Neuromuscular diseases (NMD) account for a significant proportion of infant and childhood mortality and devastating chronic disease.Determining the specific diagnosis of NMD is challenging due to thousands of unique or rare genetic variants that result in overlapping phenotypes.Our results demonstrate the utility and genetic diagnostic value of WES in the broad class of NMD phenotypes.

View Article: PubMed Central - PubMed

Affiliation: Integrated Cancer Genomics, Translational Genomics Research Institute (TGen) Phoenix, Arizona.

ABSTRACT
Neuromuscular diseases (NMD) account for a significant proportion of infant and childhood mortality and devastating chronic disease. Determining the specific diagnosis of NMD is challenging due to thousands of unique or rare genetic variants that result in overlapping phenotypes. We present four unique childhood myopathy cases characterized by relatively mild muscle weakness, slowly progressing course, mildly elevated creatine phosphokinase (CPK), and contractures. We also present two additional cases characterized by severe prenatal/neonatal myopathy. Prior extensive genetic testing and histology of these cases did not reveal the genetic etiology of disease. Here, we applied whole exome sequencing (WES) and bioinformatics to identify likely causal pathogenic variants in each pedigree. In two cases, we identified novel pathogenic variants in COL6A3. In a third case, we identified novel likely pathogenic variants in COL6A6 and COL6A3. We identified a novel splice variant in EMD in a fourth case. Finally, we classify two cases as calcium channelopathies with identification of novel pathogenic variants in RYR1 and CACNA1S. These are the first cases of myopathies reported to be caused by variants in COL6A6 and CACNA1S. Our results demonstrate the utility and genetic diagnostic value of WES in the broad class of NMD phenotypes.

No MeSH data available.


Related in: MedlinePlus