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Article: Biallelic variants in HTRA2 cause 3-methylglutaconic aciduria mitochondrial disorder: case report and literature review.

Gurusamy, Umamaheswaran / Ramadesikan, Swetha / Marhabaie, Mohammad / Colwell, Caitlyn M / Hunter, Jesse M / Leung, Marco L / Mardis, Elaine R / White, Peter / Manickam, Murugu / Wilson, Richard K / Koboldt, Daniel C

Frontiers in genetics

2024 Volume 14, Page(s) 1298574

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2024-01-18
Publishing country	Switzerland
Document type	Case Reports
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2023.1298574
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Article ; Online: Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity.

Wijeratne, Saranga / Gonzalez, Maria E Hernandez / Roach, Kelli / Miller, Katherine E / Schieffer, Kathleen M / Fitch, James R / Leonard, Jeffrey / White, Peter / Kelly, Benjamin J / Cottrell, Catherine E / Mardis, Elaine R / Wilson, Richard K / Miller, Anthony R

BMC genomics

2024 Volume 25, Issue 1, Page(s) 122

Abstract: Background: Cancers exhibit complex transcriptomes with aberrant splicing that induces isoform-level differential expression compared to non-diseased tissues. Transcriptomic profiling using short-read sequencing has utility in providing a cost-effective ...

Abstract	Background: Cancers exhibit complex transcriptomes with aberrant splicing that induces isoform-level differential expression compared to non-diseased tissues. Transcriptomic profiling using short-read sequencing has utility in providing a cost-effective approach for evaluating isoform expression, although short-read assembly displays limitations in the accurate inference of full-length transcripts. Long-read RNA sequencing (Iso-Seq), using the Pacific Biosciences (PacBio) platform, can overcome such limitations by providing full-length isoform sequence resolution which requires no read assembly and represents native expressed transcripts. A constraint of the Iso-Seq protocol is due to fewer reads output per instrument run, which, as an example, can consequently affect the detection of lowly expressed transcripts. To address these deficiencies, we developed a concatenation workflow, PacBio Full-Length Isoform Concatemer Sequencing (PB_FLIC-Seq), designed to increase the number of unique, sequenced PacBio long-reads thereby improving overall detection of unique isoforms. In addition, we anticipate that the increase in read depth will help improve the detection of moderate to low-level expressed isoforms. Results: In sequencing a commercial reference (Spike-In RNA Variants; SIRV) with known isoform complexity we demonstrated a 3.4-fold increase in read output per run and improved SIRV recall when using the PB_FLIC-Seq method compared to the same samples processed with the Iso-Seq protocol. We applied this protocol to a translational cancer case, also demonstrating the utility of the PB_FLIC-Seq method for identifying differential full-length isoform expression in a pediatric diffuse midline glioma compared to its adjacent non-malignant tissue. Our data analysis revealed increased expression of extracellular matrix (ECM) genes within the tumor sample, including an isoform of the Secreted Protein Acidic and Cysteine Rich (SPARC) gene that was expressed 11,676-fold higher than in the adjacent non-malignant tissue. Finally, by using the PB_FLIC-Seq method, we detected several cancer-specific novel isoforms. Conclusion: This work describes a concatenation-based methodology for increasing the number of sequenced full-length isoform reads on the PacBio platform, yielding improved discovery of expressed isoforms. We applied this workflow to profile the transcriptome of a pediatric diffuse midline glioma and adjacent non-malignant tissue. Our findings of cancer-specific novel isoform expression further highlight the importance of long-read sequencing for characterization of complex tumor transcriptomes.
MeSH term(s)	Humans ; Child ; Transcriptome ; Gene Expression Profiling/methods ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; RNA Splicing ; Sequence Analysis, RNA ; Glioma ; High-Throughput Nucleotide Sequencing/methods
Chemical Substances	Protein Isoforms
Language	English
Publishing date	2024-01-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-024-10021-x
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Article ; Online: The Genotypic and Phenotypic Spectrum of BICD2 Variants in Spinal Muscular Atrophy.

Koboldt, Daniel C / Waldrop, Megan A / Wilson, Richard K / Flanigan, Kevin M

Annals of neurology

2020 Volume 87, Issue 4, Page(s) 487–496

Abstract: The bicaudal D cargo adaptor 2 (BICD2) gene encodes a conserved cargo adaptor protein required for dynein-mediated transport. Inherited and de novo variants in BICD2 cause SMALED2 (spinal muscular atrophy lower extremity dominant 2), and a subset have ... ...

Abstract	The bicaudal D cargo adaptor 2 (BICD2) gene encodes a conserved cargo adaptor protein required for dynein-mediated transport. Inherited and de novo variants in BICD2 cause SMALED2 (spinal muscular atrophy lower extremity dominant 2), and a subset have recently been reported to cause severe, often lethal disease. However, a true genotype-phenotype correlation for BICD2 has not been performed, and cases described to date are scattered among at least 14 publications. In this review, we identify the characteristics of disease-causing variants in BICD2 that distinguish them from benign variation and perform genotype-phenotype correlations for 99 BICD2 variant carriers from 35 families. ANN NEUROL 2020;87:487-496.
MeSH term(s)	Genetic Association Studies ; Genotype ; Humans ; Microtubule-Associated Proteins/genetics ; Mobility Limitation ; Muscle Weakness ; Muscular Atrophy ; Mutation ; Phenotype ; Respiratory Insufficiency ; Severity of Illness Index ; Spinal Muscular Atrophies of Childhood/genetics ; Spinal Muscular Atrophies of Childhood/physiopathology
Chemical Substances	BICD2 protein, human ; Microtubule-Associated Proteins
Language	English
Publishing date	2020-02-14
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	80362-5
ISSN	1531-8249 ; 0364-5134
ISSN (online)	1531-8249
ISSN	0364-5134
DOI	10.1002/ana.25704
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Article ; Online: Novel Presentation of Hemiplegic Migraine in a Patient With Cockayne Syndrome.

Carroll, Jennifer / Pabst, Lisa / Koboldt, Daniel C / Franklin, Samuel J / Choi, Samantha / Wilson, Richard K / Lo, Warren

Pediatric neurology

2022 Volume 138, Page(s) 95–97

Abstract: Background: Cockayne syndrome is a rare DNA repair disorder marked by premature aging, poor growth, and intellectual disability. Neurological complications such as seizures, movement disorder, and stroke have been reported. Hemiplegic migraine has not ... ...

Abstract	Background: Cockayne syndrome is a rare DNA repair disorder marked by premature aging, poor growth, and intellectual disability. Neurological complications such as seizures, movement disorder, and stroke have been reported. Hemiplegic migraine has not been reported in association with Cockayne syndrome. Methods: We report a male with Cockayne syndrome due to biallelic heterozygous pathogenic variants in ERCC6 who presented repeatedly with transient focal neurological deficits and headache, which were consistent with hemiplegic migraine. Two siblings also had Cockayne syndrome and presented with similar symptoms. Results: Our patient was originally diagnosed based on clinical suspicion and then confirmed by targeted exome analysis of genes associated with Cockayne syndrome. The family's research exome sequencing data were reanalyzed to identify variants in genes known to cause familial hemiplegic migraine. No variants in the genes known to cause familial hemiplegic migraine were identified. Conclusion: This is a novel association of familial hemiplegic migraine in three full siblings with Cockayne syndrome. Hemiplegic migraine has not previously been described as part of the Cockayne syndrome presentation. A separate genetic cause of familial hemiplegic migraines was not identified in an exome-based analysis of genes known to cause this condition. This report may represent an expansion of the Cockayne syndrome phenotype.
Language	English
Publishing date	2022-10-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	639164-3
ISSN	1873-5150 ; 0887-8994
ISSN (online)	1873-5150
ISSN	0887-8994
DOI	10.1016/j.pediatrneurol.2022.10.007
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Article ; Online: A deletion in the N gene of SARS-CoV-2 may reduce test sensitivity for detection of SARS-CoV-2.

Wang, Huanyu / Jean, Sophonie / Wilson, Sarah A / Lucyshyn, Jocelyn M / McGrath, Sean / Wilson, Richard K / Magrini, Vincent / Leber, Amy L

Diagnostic microbiology and infectious disease

2021 Volume 102, Issue 4, Page(s) 115631

Abstract: One SARS-CoV-2-positive sample demonstrated impaired detection of the N1 target by RT-PCR using US CDC primer/probe sets. A 3 nucleotide deletion was discovered that overlaps the forward primer binding site. This finding underscores the importance of ... ...

Abstract	One SARS-CoV-2-positive sample demonstrated impaired detection of the N1 target by RT-PCR using US CDC primer/probe sets. A 3 nucleotide deletion was discovered that overlaps the forward primer binding site. This finding underscores the importance of continued SARS-CoV-2 mutation surveillance and assessment of the impact on diagnostic test performance.
MeSH term(s)	COVID-19/diagnosis ; DNA Primers/genetics ; Humans ; RNA, Viral/analysis ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; Sensitivity and Specificity
Chemical Substances	DNA Primers ; RNA, Viral
Language	English
Publishing date	2021-12-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	604920-5
ISSN	1879-0070 ; 0732-8893
ISSN (online)	1879-0070
ISSN	0732-8893
DOI	10.1016/j.diagmicrobio.2021.115631
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Article ; Online: Chromothripsis and human disease: piecing together the shattering process.

Maher, Christopher A / Wilson, Richard K

Cell

2012 Volume 148, Issue 1-2, Page(s) 29–32

Abstract: The unprecedented resolution of high-throughput genomics has enabled the recent discovery of a phenomenon by which specific regions of the genome are shattered and then stitched together via a single devastating event, referred to as chromothripsis. ... ...

Abstract	The unprecedented resolution of high-throughput genomics has enabled the recent discovery of a phenomenon by which specific regions of the genome are shattered and then stitched together via a single devastating event, referred to as chromothripsis. Potential mechanisms governing this process are now emerging, with implications for our understanding of the role of genomic rearrangements in development and disease.
MeSH term(s)	Chromosome Aberrations ; Genome, Human ; High-Throughput Nucleotide Sequencing ; Human Development ; Humans ; Mutation ; Neoplasms/genetics
Language	English
Publishing date	2012-01-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2012.01.006
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Article ; Online: Biallelic

Ramadesikan, Swetha / Hickey, Scott / De Los Reyes, Emily / Patel, Anup D / Franklin, Samuel J / Brennan, Patrick / Crist, Erin / Lee, Kristy / White, Peter / McBride, Kim L / Koboldt, Daniel C / Wilson, Richard K

Cold Spring Harbor molecular case studies

2022 Volume 8, Issue 2

Abstract: Noncoding and synonymous coding variants that exert their effects via alternative splicing are increasingly recognized as an important category of disease-causing variants. In this report, we describe two siblings who presented with hypotonia, profound ... ...

Abstract	Noncoding and synonymous coding variants that exert their effects via alternative splicing are increasingly recognized as an important category of disease-causing variants. In this report, we describe two siblings who presented with hypotonia, profound developmental delays, and seizures. Brain magnetic resonance imaging (MRI) in the proband at 5 yr showed diffuse cerebral and cerebellar white matter volume loss. Both siblings later developed ventilator-dependent respiratory insufficiency and scoliosis and are currently nonverbal and nonambulatory. Extensive molecular testing including oligo array and clinical exome sequencing was nondiagnostic. Research genome sequencing under an institutional review board (IRB)-approved study protocol revealed that both affected children were compound-heterozygous for variants in the
MeSH term(s)	Amino Acyl-tRNA Synthetases/genetics ; Cerebellar Diseases/genetics ; Child ; Humans ; Microcephaly/genetics ; Mutation ; Siblings
Chemical Substances	Amino Acyl-tRNA Synthetases (EC 6.1.1.-) ; O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase, human (EC 6.1.1.-)
Language	English
Publishing date	2022-03-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2835759-0
ISSN	2373-2873 ; 2373-2873
ISSN (online)	2373-2873
ISSN	2373-2873
DOI	10.1101/mcs.a006165
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Article ; Online: Inherited and de novo variants extend the etiology of

Hunter, Jesse M / Massingham, Lauren J / Manickam, Kandamurugu / Bartholomew, Dennis / Williamson, Rachel K / Schwab, Jennifer L / Marhabaie, Mohammad / Siemon, Amy / de Los Reyes, Emily / Reshmi, Shalini C / Cottrell, Catherine E / Wilson, Richard K / Koboldt, Daniel C

Cold Spring Harbor molecular case studies

2022 Volume 8, Issue 2

Abstract: Alterations in ... ...

Abstract	Alterations in the
MeSH term(s)	Child ; Developmental Disabilities/genetics ; Humans ; Intellectual Disability/genetics ; Intellectual Disability/pathology ; Muscle Hypotonia ; Neurodevelopmental Disorders/genetics ; Phenotype ; Protein Serine-Threonine Kinases/genetics ; Syndrome ; Whole Exome Sequencing
Chemical Substances	Protein Serine-Threonine Kinases (EC 2.7.11.1) ; TAO1 protein kinase (EC 2.7.11.1)
Language	English
Publishing date	2022-03-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2835759-0
ISSN	2373-2873 ; 2373-2873
ISSN (online)	2373-2873
ISSN	2373-2873
DOI	10.1101/mcs.a006180
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Article ; Online: De novo missense mutation in GRIA2 in a patient with global developmental delay, autism spectrum disorder, and epileptic encephalopathy.

Latsko, Maeson S / Koboldt, Daniel C / Franklin, Samuel J / Hickey, Scott E / Williamson, Rachel K / Garner, Shannon / Ostendorf, Adam P / Lee, Kristy / White, Peter / Wilson, Richard K

Cold Spring Harbor molecular case studies

2022

Abstract: De novo variants are increasingly recognized as a common cause of early infantile epileptic encephalopathies. We present a 4-year-old male with epileptic encephalopathy characterized by seizures, autism spectrum disorder, and global developmental delay. ... ...

Abstract	De novo variants are increasingly recognized as a common cause of early infantile epileptic encephalopathies. We present a 4-year-old male with epileptic encephalopathy characterized by seizures, autism spectrum disorder, and global developmental delay. Whole genome sequencing of the proband and his unaffected parents revealed a novel de novo missense variant in GRIA2 (c.1589A>T; p.Lys530Met; ENST00000264426.14). Variants in the GRIA2 gene were recently reported to cause an autosomal dominant neurodevelopmental disorder with language impairments and behavioral abnormalities (OMIM; MIM #618917), a condition characterized by intellectual disability and developmental delay in which seizures are a common feature. The de novo variant identified in our patient maps to the edge of a key ligand binding domain of the AMPA receptor and has not been previously reported in gnomAD or other public databases, making it novel. Our findings provided a long-sought diagnosis for this patient and support the link between GRIA2 and a dominant neurodevelopmental disorder.
Language	English
Publishing date	2022-05-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2835759-0
ISSN	2373-2873 ; 2373-2873
ISSN (online)	2373-2873
ISSN	2373-2873
DOI	10.1101/mcs.a006172
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Article ; Online: Genetic variation and the de novo assembly of human genomes.

Chaisson, Mark J P / Wilson, Richard K / Eichler, Evan E

Nature reviews. Genetics

2015 Volume 16, Issue 11, Page(s) 627–640

Abstract: The discovery of genetic variation and the assembly of genome sequences are both inextricably linked to advances in DNA-sequencing technology. Short-read massively parallel sequencing has revolutionized our ability to discover genetic variation but is ... ...

Abstract	The discovery of genetic variation and the assembly of genome sequences are both inextricably linked to advances in DNA-sequencing technology. Short-read massively parallel sequencing has revolutionized our ability to discover genetic variation but is insufficient to generate high-quality genome assemblies or resolve most structural variation. Full resolution of variation is only guaranteed by complete de novo assembly of a genome. Here, we review approaches to genome assembly, the nature of gaps or missing sequences, and biases in the assembly process. We describe the challenges of generating a complete de novo genome assembly using current technologies and the impact that being able to perfectly sequence the genome would have on understanding human disease and evolution. Finally, we summarize recent technological advances that improve both contiguity and accuracy and emphasize the importance of complete de novo assembly as opposed to read mapping as the primary means to understanding the full range of human genetic variation.
MeSH term(s)	Base Sequence ; Chromosome Mapping/methods ; Genetic Predisposition to Disease/genetics ; Genetic Variation ; Genome, Human/genetics ; Genomics/methods ; Haplotypes ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Molecular Sequence Data
Language	English
Publishing date	2015-10-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2035157-4
ISSN	1471-0064 ; 1471-0056
ISSN (online)	1471-0064
ISSN	1471-0056
DOI	10.1038/nrg3933
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Zs.MG 40: Show issues

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