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1.
J Genet Couns ; 33(1): 151-155, 2024 02.
Article in English | MEDLINE | ID: mdl-38197609

ABSTRACT

The need for education focusing on genomic technologies and variant interpretation for genetic counseling trainees has prompted genetic counseling training programs to alter their curricula to incorporate this content. Given students' diverse experiences prior to matriculation into genetic counseling training programs, students' familiarity with these topics may vary. Following receipt of feedback from trainees at a large genetic counseling program regarding an existing course focused on molecular technologies, a three-part asynchronous module series was created as a prerequisite to this course as an opportunity to align knowledge. Designed to be completed by students on their own time and at their own pace, the modules allowed for additional instruction without increases in classroom time or credit hours. Content included a refresh on genetics concepts and an introduction to available genetics resources for developing a differential diagnosis as well as variant interpretation framework. Modules utilized a clinical scenario to anchor learning with interactive content, allowing students to progress at their own pace and explore content as they found necessary. Completion of this asynchronous module series was required by incoming first-year students prior to the start of the academic semester. Following completion, students were asked to provide feedback on the module series. Reviews were primarily positive with students indicating that while the content was not entirely new, they found the review valuable and would be likely to reference the modules later in their genetic counseling training. Areas identified for improvement included additional detail regarding genetic testing methods as well as adjusting the interactive content to ensure accessibility for all students and systems. Taken together, the development and implementation of this asynchronous series as an additional component to genetic counseling training was considered a success and this approach can be considered to address additional topics dependent on a programs' needs.


Subject(s)
Genetic Counseling , Molecular Diagnostic Techniques , Humans , Students , Genetic Testing , Educational Status
2.
J Pediatr ; 262: 113620, 2023 11.
Article in English | MEDLINE | ID: mdl-37473993

ABSTRACT

OBJECTIVE: To evaluate factors influencing the diagnostic yield of comprehensive gene panel testing (CGPT) for hearing loss (HL) in children and to understand the characteristics of undiagnosed probands. STUDY DESIGN: This was a retrospective cohort study of 474 probands with childhood-onset HL who underwent CGPT between 2016 and 2020 at a single center. Main outcomes and measures included the association between clinical variables and diagnostic yield and the genetic and clinical characteristics of undiagnosed probands. RESULTS: The overall diagnostic yield was 44% (209/474) with causative variants involving 41 genes. While the diagnostic yield was high in the probands with congenital, bilateral, and severe HL, it was low in those with unilateral, noncongenital, or mild HL; cochlear nerve deficiency; preterm birth; neonatal intensive care unit admittance; certain ancestry; and developmental delay. Follow-up studies on 49 probands with initially inconclusive CGPT results changed the diagnostic status to likely positive or negative outcomes in 39 of them (80%). Reflex to exome sequencing on 128 undiagnosed probands by CGPT revealed diagnostic findings in 8 individuals, 5 of whom had developmental delays. The remaining 255 probands were undiagnosed, with 173 (173/255) having only a single variant in the gene(s) associated with autosomal recessive HL and 28% (48/173) having a matched phenotype. CONCLUSION: CGPT efficiently identifies the genetic etiologies of HL in children. CGPT-undiagnosed probands may benefit from follow-up studies or expanded testing.


Subject(s)
Deafness , Hearing Loss, Sensorineural , Hearing Loss , Premature Birth , Female , Humans , Child , Infant, Newborn , Retrospective Studies , Premature Birth/genetics , Hearing Loss/diagnosis , Hearing Loss/genetics , Deafness/genetics , Phenotype , Hearing Loss, Sensorineural/diagnosis , Genetic Testing/methods
3.
Hum Mutat ; 43(12): 1837-1843, 2022 12.
Article in English | MEDLINE | ID: mdl-35870179

ABSTRACT

Synonymous variants have been shown to alter the correct splicing of pre-mRNAs and generate disease-causing transcripts. These variants are not an uncommon etiology of genetic disease; however, they are frequently overlooked during genetic testing in the absence of functional and clinical data. Here, we describe the occurrence of a synonymous variant [NM_005422.4 (TECTA):c.327C>T, p.(Gly109=)] in seven individuals with hearing loss from six unrelated families. The variant is not located near exonic/intronic boundaries but is predicted to impact splicing by activating a cryptic splicing donor site in exon 4 of TECTA. In vitro minigene assays show that the variant disrupts the reading frame of the canonical transcript, which is predicted to cause a premature termination codon 48 amino acids downstream of the variant, leading to nonsense-mediated decay. The variant is present in population databases, predominantly in Latinos of African ancestry, but is rare in other ethnic groups. Our findings suggest that this synonymous variant is likely pathogenic for TECTA-associated autosomal recessive hearing loss and seems to have arisen as a founder variant in this specific Latino subpopulation. This study demonstrates that synonymous variants need careful splicing assessment and support from additional testing methodologies to determine their clinical impact.


Subject(s)
Deafness , Hearing Loss , Humans , RNA Splice Sites , RNA Splicing/genetics , Hearing Loss/genetics , Deafness/genetics , Exons/genetics , Extracellular Matrix Proteins/genetics , GPI-Linked Proteins/genetics
4.
J Mol Diagn ; 24(3): 274-286, 2022 03.
Article in English | MEDLINE | ID: mdl-35065284

ABSTRACT

Clinical exome sequencing (CES) aids in the diagnosis of rare genetic disorders. Herein, we report the molecular diagnostic yield and spectrum of genetic alterations contributing to disease in 700 pediatric cases analyzed at the Children's Hospital of Philadelphia. The overall diagnostic yield was 23%, with three cases having more than one molecular diagnosis and 2.6% having secondary/additional findings. A candidate gene finding was reported in another 8.4% of cases. The clinical indications with the highest diagnostic yield were neurodevelopmental disorders (including seizures), whereas immune- and oncology-related indications were negatively associated with molecular diagnosis. The rapid expansion of knowledge regarding the genome's role in human disease necessitates reanalysis of CES samples. To capture these new discoveries, a subset of cases (n = 240) underwent reanalysis, with an increase in diagnostic yield. We describe our experience reporting CES results in a pediatric setting, including reporting of secondary findings, reporting newly discovered genetic conditions, and revisiting negative test results. Finally, we highlight the challenges associated with implementing critical updates to the CES workflow. Although these updates are necessary, they demand an investment of time and resources from the laboratory. In summary, these data demonstrate the clinical utility of exome sequencing and reanalysis, while highlighting the critical considerations for continuous improvement of a CES test in a clinical laboratory.


Subject(s)
Exome , Pathology, Molecular , Child , Exome/genetics , Humans , Mutation , Rare Diseases/genetics , Retrospective Studies , Exome Sequencing/methods
5.
Am J Hum Genet ; 106(6): 830-845, 2020 06 04.
Article in English | MEDLINE | ID: mdl-32442410

ABSTRACT

SOX6 belongs to a family of 20 SRY-related HMG-box-containing (SOX) genes that encode transcription factors controlling cell fate and differentiation in many developmental and adult processes. For SOX6, these processes include, but are not limited to, neurogenesis and skeletogenesis. Variants in half of the SOX genes have been shown to cause severe developmental and adult syndromes, referred to as SOXopathies. We here provide evidence that SOX6 variants also cause a SOXopathy. Using clinical and genetic data, we identify 19 individuals harboring various types of SOX6 alterations and exhibiting developmental delay and/or intellectual disability; the individuals are from 17 unrelated families. Additional, inconstant features include attention-deficit/hyperactivity disorder (ADHD), autism, mild facial dysmorphism, craniosynostosis, and multiple osteochondromas. All variants are heterozygous. Fourteen are de novo, one is inherited from a mosaic father, and four offspring from two families have a paternally inherited variant. Intragenic microdeletions, balanced structural rearrangements, frameshifts, and nonsense variants are predicted to inactivate the SOX6 variant allele. Four missense variants occur in residues and protein regions highly conserved evolutionarily. These variants are not detected in the gnomAD control cohort, and the amino acid substitutions are predicted to be damaging. Two of these variants are located in the HMG domain and abolish SOX6 transcriptional activity in vitro. No clear genotype-phenotype correlations are found. Taken together, these findings concur that SOX6 haploinsufficiency leads to a neurodevelopmental SOXopathy that often includes ADHD and abnormal skeletal and other features.


Subject(s)
Attention Deficit Disorder with Hyperactivity/genetics , Craniosynostoses/genetics , Neurodevelopmental Disorders/genetics , Osteochondroma/genetics , SOXD Transcription Factors/genetics , Active Transport, Cell Nucleus , Adolescent , Amino Acid Sequence , Base Sequence , Brain/embryology , Brain/growth & development , Brain/metabolism , Child , Child, Preschool , Computer Simulation , Female , Genomic Structural Variation/genetics , Humans , Infant , Male , Mutation, Missense , Neurodevelopmental Disorders/diagnosis , RNA-Seq , SOXD Transcription Factors/chemistry , SOXD Transcription Factors/metabolism , Syndrome , Transcription, Genetic , Transcriptome , Translocation, Genetic/genetics
6.
Genet Med ; 22(2): 389-397, 2020 02.
Article in English | MEDLINE | ID: mdl-31388190

ABSTRACT

PURPOSE: Sifrim-Hitz-Weiss syndrome (SIHIWES) is a recently described multisystemic neurodevelopmental disorder caused by de novo variants inCHD4. In this study, we investigated the clinical spectrum of the disorder, genotype-phenotype correlations, and the effect of different missense variants on CHD4 function. METHODS: We collected clinical and molecular data from 32 individuals with mostly de novo variants in CHD4, identified through next-generation sequencing. We performed adenosine triphosphate (ATP) hydrolysis and nucleosome remodeling assays on variants from five different CHD4 domains. RESULTS: The majority of participants had global developmental delay, mild to moderate intellectual disability, brain anomalies, congenital heart defects, and dysmorphic features. Macrocephaly was a frequent but not universal finding. Additional common abnormalities included hypogonadism in males, skeletal and limb anomalies, hearing impairment, and ophthalmic abnormalities. The majority of variants were nontruncating and affected the SNF2-like region of the protein. We did not identify genotype-phenotype correlations based on the type or location of variants. Alterations in ATP hydrolysis and chromatin remodeling activities were observed in variants from different domains. CONCLUSION: The CHD4-related syndrome is a multisystemic neurodevelopmental disorder. Missense substitutions in different protein domains alter CHD4 function in a variant-specific manner, but result in a similar phenotype in humans.


Subject(s)
Mi-2 Nucleosome Remodeling and Deacetylase Complex/genetics , Neurodevelopmental Disorders/genetics , Abnormalities, Multiple/genetics , Adolescent , Adult , Child , Child, Preschool , Chromatin Assembly and Disassembly/genetics , Developmental Disabilities/genetics , Female , Genetic Association Studies , Genotype , Hearing Loss/genetics , Heart Defects, Congenital/genetics , Humans , Infant , Infant, Newborn , Intellectual Disability/genetics , Male , Megalencephaly/genetics , Mi-2 Nucleosome Remodeling and Deacetylase Complex/metabolism , Musculoskeletal Abnormalities/genetics , Mutation, Missense/genetics , Phenotype , Syndrome , Transcription Factors/genetics
8.
JAMA Netw Open ; 2(4): e192129, 2019 04 05.
Article in English | MEDLINE | ID: mdl-30977854

ABSTRACT

Importance: Although genetic testing is important for bringing precision medicine to children with epilepsy, it is unclear what genetic testing strategy is best in maximizing diagnostic yield. Objectives: To evaluate the diagnostic yield of an exome-based gene panel for childhood epilepsy and discuss the value of follow-up testing. Design, Setting, and Participants: A case series study was conducted on data from clinical genetic testing at Children's Hospital of Philadelphia was conducted from September 26, 2016, to January 8, 2018. Initial testing targeted 100 curated epilepsy genes for sequence and copy number analysis in 151 children with idiopathic epilepsy referred consecutively by neurologists. Additional genetic testing options were offered afterward. Exposures: Clinical genetic testing. Main Outcomes and Measures: Molecular diagnostic findings. Results: Of 151 patients (84 boys [55.6%]; median age, 4.2 years [interquartile range, 1.4-8.7 years]), 16 children (10.6%; 95% CI, 6%-16%) received a diagnosis after initial panel analysis. Parental testing for 15 probands with inconclusive results revealed de novo variants in 7 individuals (46.7%), resulting in an overall diagnostic yield of 15.3% (23 of 151; 95% CI, 9%-21%). Twelve probands with nondiagnostic panel findings were reflexed to exome sequencing, and 4 were diagnostic (33.3%; 95% CI, 6%-61%), raising the overall diagnostic yield to 17.9% (27 of 151; 95% CI, 12%-24%). The yield was highest (17 of 44 [38.6%; 95% CI, 24%-53%]) among probands with epilepsy onset in infancy (age, 1-12 months). Panel diagnostic findings involved 16 genes: SCN1A (n = 4), PRRT2 (n = 3), STXBP1 (n = 2), IQSEC2 (n = 2), ATP1A2, ATP1A3, CACNA1A, GABRA1, KCNQ2, KCNT1, SCN2A, SCN8A, DEPDC5, TPP1, PCDH19, and UBE3A (all n = 1). Exome sequencing analysis identified 4 genes: SMC1A, SETBP1, NR2F1, and TRIT1. For the remaining 124 patients, analysis of 13 additional genes implicated in epilepsy since the panel was launched in 2016 revealed promising findings in 6 patients. Conclusions and Relevance: Exome-based targeted panels appear to enable rapid analysis of a preselected set of genes while retaining flexibility in gene content. Successive genetic workup should include parental testing of select probands with inconclusive results and reflex to whole-exome trio analysis for the remaining nondiagnostic cases. Periodic reanalysis is needed to capture information in newly identified disease genes.


Subject(s)
Epilepsy/diagnosis , Epilepsy/genetics , Exome Sequencing/methods , Genetic Predisposition to Disease/genetics , Genetic Testing/methods , Child , Child, Preschool , Female , Humans , Infant , Male , Tripeptidyl-Peptidase 1
9.
Am J Med Genet A ; 179(3): 365-372, 2019 03.
Article in English | MEDLINE | ID: mdl-30588760

ABSTRACT

MYH7-related disease (MRD) is the most common hereditary primary cardiomyopathy (CM), with pathogenic MYH7 variants accounting for approximately 40% of familial hypertrophic CMs. MRDs may also present as skeletal myopathies, with or without CM. Since pathogenic MYH7 variants result in highly variable clinical phenotypes, from mild to fatal forms of cardiac and skeletal myopathies, genotype-phenotype correlations are not always apparent, and translation of the genetic findings to clinical practice can be complicated. Data on genotype-phenotype correlations can help facilitate more specific and personalized decisions on treatment strategies, surveillance, and genetic counseling. We present a series of six MRD pedigrees with rare genotypes, encompassing various clinical presentations and inheritance patterns. This study provides new insights into the spectrum of MRD that is directly translatable to clinical practice.


Subject(s)
Cardiac Myosins/genetics , Cardiomyopathies/diagnosis , Cardiomyopathies/genetics , Genetic Association Studies , Genotype , Mutation , Myosin Heavy Chains/genetics , Phenotype , Adult , Biological Variation, Population , Biopsy , Child , Child, Preschool , DNA Mutational Analysis , Echocardiography , Humans , Infant , Inheritance Patterns , Karyotyping , Pedigree
10.
J Mol Diagn ; 21(1): 38-48, 2019 01.
Article in English | MEDLINE | ID: mdl-30577886

ABSTRACT

Clinical exome sequencing (CES) has a reported diagnostic yield of 20% to 30% for most clinical indications. The ongoing discovery of novel gene-disease and variant-disease associations are expected to increase the diagnostic yield of CES. Performing systematic reanalysis of previously nondiagnostic CES samples represents a significant challenge for clinical laboratories. Here, we present the results of a novel automated reanalysis methodology applied to 300 CES samples initially analyzed between June 2014 and September 2016. Application of our reanalysis methodology reduced reanalysis variant analysis burden by >93% and correctly captured 70 of 70 previously identified diagnostic variants among 60 samples with previously identified diagnoses. Notably, reanalysis of 240 initially nondiagnostic samples using information available on July 1, 2017, revealed 38 novel diagnoses, representing a 15.8% increase in diagnostic yield. Modeling monthly iterative reanalysis of 240 nondiagnostic samples revealed a diagnostic rate of 0.57% of samples per month. Modeling the workload required for monthly iterative reanalysis of nondiagnostic samples revealed a variant analysis burden of approximately 5 variants/month for proband-only and approximately 0.5 variants/month for trio samples. Approximately 45% of samples required evaluation during each monthly interval, and 61.3% of samples were reevaluated across three consecutive reanalyses. In sum, automated reanalysis methods can facilitate efficient reevaluation of nondiagnostic samples using up-to-date literature and can provide significant value to clinical laboratories.


Subject(s)
Exome Sequencing/methods , DNA/genetics , Exome , Female , Genetic Testing/methods , Genetic Variation , Humans , Male
12.
Epilepsy Res ; 145: 89-92, 2018 09.
Article in English | MEDLINE | ID: mdl-29933145

ABSTRACT

Heterozygous de novo or inherited pathogenic variants in the PCDH19 gene cause a spectrum of neurodevelopmental features including developmental delay and seizures. PCDH19 epilepsy was previously known as "epilepsy and mental retardation limited to females", since the condition almost exclusively affects females. It is hypothesized that the co-existence of two populations of neurons, some with and some without PCDH19 protein expression, results in pathologically abnormal interactions between these neurons, a mechanism also referred to as cellular interference. Consequently, PCDH19-related epilepsies are inherited in an atypical X-linked pattern, such that hemizygous, non-mosaic, 46,XY males are typically unaffected, while individuals with a disease-causing PCDH19 variant, mainly heterozygous females and mosaic males, are affected. As a corollary to this hypothesis, an individual with Klinefelter syndrome (KS) (47,XXY) who has a heterozygous disease-causing PCDH19 variant should develop PCDH19-related epilepsy. Here, we report such evidence: - a male child with KS and PCDH19-related epilepsy - supporting the PCDH19 cellular interference disease hypothesis.


Subject(s)
Cadherins/genetics , Epilepsy/genetics , Epilepsy/pathology , Klinefelter Syndrome/genetics , Klinefelter Syndrome/pathology , Child, Preschool , Chromosomes, Human, X/genetics , Epilepsy/complications , Epilepsy/rehabilitation , Humans , Klinefelter Syndrome/complications , Klinefelter Syndrome/rehabilitation , Male , Protocadherins
13.
Genet Med ; 20(12): 1663-1676, 2018 12.
Article in English | MEDLINE | ID: mdl-29907799

ABSTRACT

PURPOSE: Hearing loss (HL) is the most common sensory disorder in children. Prompt molecular diagnosis may guide screening and management, especially in syndromic cases when HL is the single presenting feature. Exome sequencing (ES) is an appealing diagnostic tool for HL as the genetic causes are highly heterogeneous. METHODS: ES was performed on a prospective cohort of 43 probands with HL. Sequence data were analyzed for primary and secondary findings. Capture and coverage analysis was performed for genes and variants associated with HL. RESULTS: The diagnostic rate using ES was 37.2%, compared with 15.8% for the clinical HL panel. Secondary findings were discovered in three patients. For 247 genes associated with HL, 94.7% of the exons were targeted for capture and 81.7% of these exons were covered at 20× or greater. Further analysis of 454 randomly selected HL-associated variants showed that 89% were targeted for capture and 75% were covered at a read depth of at least 20×. CONCLUSION: ES has an improved yield compared with clinical testing and may capture diagnoses not initially considered due to subtle clinical phenotypes. Technical challenges were identified, including inadequate capture and coverage of HL genes. Additional considerations of ES include secondary findings, cost, and turnaround time.


Subject(s)
Exome Sequencing , Hearing Loss/genetics , High-Throughput Nucleotide Sequencing , Pathology, Molecular , Child, Preschool , Exome/genetics , Female , Hearing Loss/diagnosis , Hearing Loss/pathology , Humans , Infant , Infant, Newborn , Male , Mutation , Phenotype
14.
Genet Med ; 20(3): 329-336, 2018 03.
Article in English | MEDLINE | ID: mdl-29389922

ABSTRACT

PurposeThe objective of this study was to assess the ability of our laboratory's exome-sequencing test to detect known and novel sequence variants and identify the critical factors influencing the interpretation of a clinical exome test.MethodsWe developed a two-tiered validation strategy: (i) a method-based approach that assessed the ability of our exome test to detect known variants using a reference HapMap sample, and (ii) an interpretation-based approach that assessed our relative ability to identify and interpret disease-causing variants, by analyzing and comparing the results of 19 randomly selected patients previously tested by external laboratories.ResultsWe demonstrate that this approach is reproducible with >99% analytical sensitivity and specificity for single-nucleotide variants and indels <10 bp. Our findings were concordant with the reference laboratories in 84% of cases. A new molecular diagnosis was applied to three cases, including discovery of two novel candidate genes.ConclusionWe provide an assessment of critical areas that influence interpretation of an exome test, including comprehensive phenotype capture, assessment of clinical overlap, availability of parental data, and the addressing of limitations in database updates. These results can be used to inform improvements in phenotype-driven interpretation of medical exomes in clinical and research settings.


Subject(s)
Data Accuracy , Exome , Genetic Testing , High-Throughput Nucleotide Sequencing , Sequence Analysis, DNA , Computational Biology/methods , Genetic Association Studies , Genetic Predisposition to Disease , Genetic Testing/methods , Genetic Testing/standards , Genomics/methods , Genomics/standards , Humans , INDEL Mutation , Polymorphism, Single Nucleotide , Reproducibility of Results , Sensitivity and Specificity
16.
Hum Genomics ; 9: 15, 2015 Jul 19.
Article in English | MEDLINE | ID: mdl-26187847

ABSTRACT

BACKGROUND: Conditions associated with sudden cardiac arrest/death (SCA/D) in youth often have a genetic etiology. While SCA/D is uncommon, a pro-active family screening approach may identify these inherited structural and electrical abnormalities prior to symptomatic events and allow appropriate surveillance and treatment. This study investigated the diagnostic utility of exome sequencing (ES) by evaluating the capture and coverage of genes related to SCA/D. METHODS: Samples from 102 individuals (13 with known molecular etiologies for SCA/D, 30 individuals without known molecular etiologies for SCA/D and 59 with other conditions) were analyzed following exome capture and sequencing at an average read depth of 100X. Reads were mapped to human genome GRCh37 using Novoalign, and post-processing and analysis was done using Picard and GATK. A total of 103 genes (2,190 exons) related to SCA/D were used as a primary filter. An additional 100 random variants within the targeted genes associated with SCA/D were also selected and evaluated for depth of sequencing and coverage. Although the primary objective was to evaluate the adequacy of depth of sequencing and coverage of targeted SCA/D genes and not for primary diagnosis, all patients who had SCA/D (known or unknown molecular etiologies) were evaluated with the project's variant analysis pipeline to determine if the molecular etiologies could be successfully identified. RESULTS: The majority of exons (97.6 %) were captured and fully covered on average at minimum of 20x sequencing depth. The proportion of unique genomic positions reported within poorly covered exons remained small (4 %). Exonic regions with less coverage reflect the need to enrich these areas to improve coverage. Despite limitations in coverage, we identified 100 % of cases with a prior known molecular etiology for SCA/D, and analysis of an additional 30 individuals with SCA/D but no known molecular etiology revealed a diagnostic answer in 5/30 (17 %). We also demonstrated 95 % of 100 randomly selected reported variants within our targeted genes would have been picked up on ES based on our coverage analysis. CONCLUSIONS: ES is a helpful clinical diagnostic tool for SCA/D given its potential to successfully identify a molecular diagnosis, but clinicians should be aware of limitations of available platforms from technical and diagnostic perspectives.


Subject(s)
Death, Sudden, Cardiac , Exome/genetics , Genomics , High-Throughput Nucleotide Sequencing/methods , Adolescent , Alleles , Child , Genome, Human , Humans , Sequence Analysis, DNA , Young Adult
17.
BMC Bioinformatics ; 15: 248, 2014 Jul 21.
Article in English | MEDLINE | ID: mdl-25047600

ABSTRACT

BACKGROUND: Exome sequencing is a promising method for diagnosing patients with a complex phenotype. However, variant interpretation relative to patient phenotype can be challenging in some scenarios, particularly clinical assessment of rare complex phenotypes. Each patient's sequence reveals many possibly damaging variants that must be individually assessed to establish clear association with patient phenotype. To assist interpretation, we implemented an algorithm that ranks a given set of genes relative to patient phenotype. The algorithm orders genes by the semantic similarity computed between phenotypic descriptors associated with each gene and those describing the patient. Phenotypic descriptor terms are taken from the Human Phenotype Ontology (HPO) and semantic similarity is derived from each term's information content. RESULTS: Model validation was performed via simulation and with clinical data. We simulated 33 Mendelian diseases with 100 patients per disease. We modeled clinical conditions by adding noise and imprecision, i.e. phenotypic terms unrelated to the disease and terms less specific than the actual disease terms. We ranked the causative gene against all 2488 HPO annotated genes. The median causative gene rank was 1 for the optimal and noise cases, 12 for the imprecision case, and 60 for the imprecision with noise case. Additionally, we examined a clinical cohort of subjects with hearing impairment. The disease gene median rank was 22. However, when also considering the patient's exome data and filtering non-exomic and common variants, the median rank improved to 3. CONCLUSIONS: Semantic similarity can rank a causative gene highly within a gene list relative to patient phenotype characteristics, provided that imprecision is mitigated. The clinical case results suggest that phenotype rank combined with variant analysis provides significant improvement over the individual approaches. We expect that this combined prioritization approach may increase accuracy and decrease effort for clinical genetic diagnosis.


Subject(s)
Biological Ontologies , Computational Biology/methods , Data Mining/methods , Disease/genetics , Phenotype , Semantics , Algorithms , Databases, Genetic , Exome/genetics , Humans , Software
18.
Hum Mutat ; 35(7): 868-79, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24664454

ABSTRACT

Laing early onset distal myopathy and myosin storage myopathy are caused by mutations of slow skeletal/ß-cardiac myosin heavy chain encoded by the gene MYH7, as is a common form of familial hypertrophic/dilated cardiomyopathy. The mechanisms by which different phenotypes are produced by mutations in MYH7, even in the same region of the gene, are not known. To explore the clinical spectrum and pathobiology, we screened the MYH7 gene in 88 patients from 21 previously unpublished families presenting with distal or generalized skeletal muscle weakness, with or without cardiac involvement. Twelve novel mutations have been identified in thirteen families. In one of these families, the father of the proband was found to be a mosaic for the MYH7 mutation. In eight cases, de novo mutation appeared to have occurred, which was proven in four. The presenting complaint was footdrop, sometimes leading to delayed walking or tripping, in members of 17 families (81%), with other presentations including cardiomyopathy in infancy, generalized floppiness, and scoliosis. Cardiac involvement as well as skeletal muscle weakness was identified in nine of 21 families. Spinal involvement such as scoliosis or rigidity was identified in 12 (57%). This report widens the clinical and pathological phenotypes, and the genetics of MYH7 mutations leading to skeletal muscle diseases.


Subject(s)
Cardiac Myosins/genetics , Distal Myopathies/diagnosis , Distal Myopathies/genetics , Mutation , Myosin Heavy Chains/genetics , Phenotype , Adolescent , Adult , Aged , Biopsy , Cardiac Myosins/metabolism , Child , Child, Preschool , DNA Mutational Analysis , Female , Humans , Immunohistochemistry , Infant , Infant, Newborn , Male , Middle Aged , Muscle, Skeletal/pathology , Myosin Heavy Chains/metabolism , Young Adult
19.
Genome Biol ; 15(3): R53, 2014 Mar 25.
Article in English | MEDLINE | ID: mdl-24667040

ABSTRACT

BACKGROUND: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.


Subject(s)
Databases, Genetic/standards , Genetic Testing/methods , Genomics/methods , Peer Review, Research , Sequence Analysis, DNA/methods , Child , Female , Financing, Organized , Genetic Testing/economics , Genetic Testing/standards , Genomics/economics , Genomics/standards , Heart Defects, Congenital/diagnosis , Heart Defects, Congenital/genetics , Humans , Male , Myopathies, Structural, Congenital/diagnosis , Myopathies, Structural, Congenital/genetics , Sequence Analysis, DNA/economics , Sequence Analysis, DNA/standards
20.
Genet Med ; 15(11): 860-7, 2013 Nov.
Article in English | MEDLINE | ID: mdl-24195999

ABSTRACT

As genomic and exomic testing expands in both the research and clinical arenas, determining whether, how, and which incidental findings to return to the ordering clinician and patient becomes increasingly important. Although opinion is varied on what should be returned to consenting patients or research participants, most experts agree that return of medically actionable results should be considered. There is insufficient evidence to fully inform evidence-based clinical practice guidelines regarding return of results from genome-scale sequencing, and thus generation of such evidence is imperative, given the rapidity with which genome-scale diagnostic tests are being incorporated into clinical care. We present an overview of the approaches to incidental findings by members of the Clinical Sequencing Exploratory Research network, funded by the National Human Genome Research Institute, to generate discussion of these approaches by the clinical genomics community. We also report specific lists of "medically actionable" genes that have been generated by a subset of investigators in order to explore what types of findings have been included or excluded in various contexts. A discussion of the general principles regarding reporting of novel variants, challenging cases (genes for which consensus was difficult to achieve across Clinical Sequencing Exploratory Research network sites), solicitation of preferences from participants regarding return of incidental findings, and the timing and context of return of incidental findings are provided.Genet Med 15 11, 860-867.Genetics in Medicine (2013); 15 11, 860-867. doi:10.1038/gim.2013.133.


Subject(s)
Genetic Testing , Genome, Human , Genomics , Incidental Findings , Sequence Analysis, DNA , Adult , Child , Exome , Genetic Variation , Genetics, Medical , Humans , National Human Genome Research Institute (U.S.) , Patient Preference , United States
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