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1.
Am J Hum Genet ; 109(9): 1605-1619, 2022 09 01.
Article in English | MEDLINE | ID: mdl-36007526

ABSTRACT

Newborn screening (NBS) dramatically improves outcomes in severe childhood disorders by treatment before symptom onset. In many genetic diseases, however, outcomes remain poor because NBS has lagged behind drug development. Rapid whole-genome sequencing (rWGS) is attractive for comprehensive NBS because it concomitantly examines almost all genetic diseases and is gaining acceptance for genetic disease diagnosis in ill newborns. We describe prototypic methods for scalable, parentally consented, feedback-informed NBS and diagnosis of genetic diseases by rWGS and virtual, acute management guidance (NBS-rWGS). Using established criteria and the Delphi method, we reviewed 457 genetic diseases for NBS-rWGS, retaining 388 (85%) with effective treatments. Simulated NBS-rWGS in 454,707 UK Biobank subjects with 29,865 pathogenic or likely pathogenic variants associated with 388 disorders had a true negative rate (specificity) of 99.7% following root cause analysis. In 2,208 critically ill children with suspected genetic disorders and 2,168 of their parents, simulated NBS-rWGS for 388 disorders identified 104 (87%) of 119 diagnoses previously made by rWGS and 15 findings not previously reported (NBS-rWGS negative predictive value 99.6%, true positive rate [sensitivity] 88.8%). Retrospective NBS-rWGS diagnosed 15 children with disorders that had been undetected by conventional NBS. In 43 of the 104 children, had NBS-rWGS-based interventions been started on day of life 5, the Delphi consensus was that symptoms could have been avoided completely in seven critically ill children, mostly in 21, and partially in 13. We invite groups worldwide to refine these NBS-rWGS conditions and join us to prospectively examine clinical utility and cost effectiveness.


Subject(s)
Neonatal Screening , Precision Medicine , Child , Critical Illness , Genetic Testing/methods , Humans , Infant, Newborn , Neonatal Screening/methods , Retrospective Studies
2.
Am J Med Genet A ; 191(4): 930-940, 2023 04.
Article in English | MEDLINE | ID: mdl-36651673

ABSTRACT

Increasing use of unbiased genomic sequencing in critically ill infants can expand understanding of rare diseases such as Kabuki syndrome (KS). Infants diagnosed with KS through genome-wide sequencing performed during the initial hospitalization underwent retrospective review of medical records. Human phenotype ontology terms used in genomic analysis were aggregated and analyzed. Clinicians were surveyed regarding changes in management and other care changes. Fifteen infants met inclusion criteria. KS was not suspected prior to genomic sequencing. Variants were classified as Pathogenic (n = 10) or Likely Pathogenic (n = 5) by American College of Medical Genetics and Genomics Guidelines. Fourteen variants were de novo (KMT2D, n = 12, KDM6A, n = 2). One infant inherited a likely pathogenic variant in KMT2D from an affected father. Frequent findings involved cardiovascular (14/15) and renal (7/15) systems, with palatal defects also identified (6/15). Three infants had non-immune hydrops. No minor anomalies were universally documented; ear anomalies, micrognathia, redundant nuchal skin, and hypoplastic nails were common. Changes in management were reported in 14 infants. Early use of unbiased genome-wide sequencing enabled a molecular diagnosis prior to clinical recognition including infants with atypical or rarely reported features of KS while also expanding the phenotypic spectrum of this rare disorder.


Subject(s)
Abnormalities, Multiple , Hematologic Diseases , Vestibular Diseases , Pregnancy , Female , Humans , Infant , Abnormalities, Multiple/genetics , Face/abnormalities , Hematologic Diseases/genetics , Vestibular Diseases/genetics , Phenotype , Histone Demethylases/genetics
3.
J Med Genet ; 59(11): 1058-1068, 2022 11.
Article in English | MEDLINE | ID: mdl-35232796

ABSTRACT

BACKGROUND: A neurodevelopmental syndrome was recently reported in four patients with SOX4 heterozygous missense variants in the high-mobility-group (HMG) DNA-binding domain. The present study aimed to consolidate clinical and genetic knowledge of this syndrome. METHODS: We newly identified 17 patients with SOX4 variants, predicted variant pathogenicity using in silico tests and in vitro functional assays and analysed the patients' phenotypes. RESULTS: All variants were novel, distinct and heterozygous. Seven HMG-domain missense and five stop-gain variants were classified as pathogenic or likely pathogenic variant (L/PV) as they precluded SOX4 transcriptional activity in vitro. Five HMG-domain and non-HMG-domain missense variants were classified as of uncertain significance (VUS) due to negative results from functional tests. When known, inheritance was de novo or from a mosaic unaffected or non-mosaic affected parent for patients with L/PV, and from a non-mosaic asymptomatic or affected parent for patients with VUS. All patients had neurodevelopmental, neurological and dysmorphic features, and at least one cardiovascular, ophthalmological, musculoskeletal or other somatic anomaly. Patients with L/PV were overall more affected than patients with VUS. They resembled patients with other neurodevelopmental diseases, including the SOX11-related and Coffin-Siris (CSS) syndromes, but lacked the most specific features of CSS. CONCLUSION: These findings consolidate evidence of a fairly non-specific neurodevelopmental syndrome due to SOX4 haploinsufficiency in neurogenesis and multiple other developmental processes.


Subject(s)
Hand Deformities, Congenital , Intellectual Disability , Micrognathism , Neurodevelopmental Disorders , Humans , Micrognathism/genetics , Hand Deformities, Congenital/genetics , Intellectual Disability/genetics , Neurodevelopmental Disorders/genetics , Syndrome , Phenotype , DNA , SOXC Transcription Factors/genetics
4.
Am J Hum Genet ; 105(4): 719-733, 2019 10 03.
Article in English | MEDLINE | ID: mdl-31564432

ABSTRACT

The second Newborn Sequencing in Genomic Medicine and Public Health study was a randomized, controlled trial of the effectiveness of rapid whole-genome or -exome sequencing (rWGS or rWES, respectively) in seriously ill infants with diseases of unknown etiology. Here we report comparisons of analytic and diagnostic performance. Of 1,248 ill inpatient infants, 578 (46%) had diseases of unknown etiology. 213 infants (37% of those eligible) were enrolled within 96 h of admission. 24 infants (11%) were very ill and received ultra-rapid whole-genome sequencing (urWGS). The remaining infants were randomized, 95 to rWES and 94 to rWGS. The analytic performance of rWGS was superior to rWES, including variants likely to affect protein function, and ClinVar pathogenic/likely pathogenic variants (p < 0.0001). The diagnostic performance of rWGS and rWES were similar (18 diagnoses in 94 infants [19%] versus 19 diagnoses in 95 infants [20%], respectively), as was time to result (median 11.0 versus 11.2 days, respectively). However, the proportion diagnosed by urWGS (11 of 24 [46%]) was higher than rWES/rWGS (p = 0.004) and time to result was less (median 4.6 days, p < 0.0001). The incremental diagnostic yield of reflexing to trio after negative proband analysis was 0.7% (1 of 147). In conclusion, rapid genomic sequencing can be performed as a first-tier diagnostic test in inpatient infants. urWGS had the shortest time to result, which was important in unstable infants, and those in whom a genetic diagnosis was likely to impact immediate management. Further comparison of urWGS and rWES is warranted because genomic technologies and knowledge of variant pathogenicity are evolving rapidly.


Subject(s)
Exome Sequencing , Whole Genome Sequencing , Genetic Testing , Humans , Infant , Infant, Newborn
5.
Am J Hum Genet ; 103(1): 154-162, 2018 07 05.
Article in English | MEDLINE | ID: mdl-29961569

ABSTRACT

TRAF7 is a multi-functional protein involved in diverse signaling pathways and cellular processes. The phenotypic consequence of germline TRAF7 variants remains unclear. Here we report missense variants in TRAF7 in seven unrelated individuals referred for clinical exome sequencing. The seven individuals share substantial phenotypic overlap, with developmental delay, congenital heart defects, limb and digital anomalies, and dysmorphic features emerging as key unifying features. The identified variants are de novo in six individuals and comprise four distinct missense changes, including a c.1964G>A (p.Arg655Gln) variant that is recurrent in four individuals. These variants affect evolutionarily conserved amino acids and are located in key functional domains. Gene-specific mutation rate analysis showed that the occurrence of the de novo variants in TRAF7 (p = 2.6 × 10-3) and the recurrent de novo c.1964G>A (p.Arg655Gln) variant (p = 1.9 × 10-8) in our exome cohort was unlikely to have occurred by chance. In vitro analyses of the observed TRAF7 mutations showed reduced ERK1/2 phosphorylation. Our findings suggest that missense mutations in TRAF7 are associated with a multisystem disorder and provide evidence of a role for TRAF7 in human development.


Subject(s)
Developmental Disabilities/genetics , Intellectual Disability/genetics , Mutation, Missense/genetics , Tumor Necrosis Factor Receptor-Associated Peptides and Proteins/genetics , Adult , Amino Acids/genetics , Child , Child, Preschool , Exome/genetics , Female , Heart Defects, Congenital/genetics , Humans , Infant , Infant, Newborn , MAP Kinase Signaling System/genetics , Male , Musculoskeletal Abnormalities/genetics , Phenotype
7.
J Clin Immunol ; 41(6): 1241-1249, 2021 08.
Article in English | MEDLINE | ID: mdl-33855675

ABSTRACT

PURPOSE: IKAROS, encoded by IKZF1, is a member of the IKAROS family of zinc-finger transcription factors playing critical roles in lymphocyte development, differentiation, and tumor suppression. Several studies demonstrated that IKZF1 mutations affecting DNA binding or homo-/hetero-dimerization are mostly associated with common variable immunodeficiency, combined immunodeficiency, or hematologic manifestations. Herein we report a likely de novo, nonsense IKZF1 mutation (p.C182*) in a baby with low T cell receptor excision circles (TREC) identified by newborn screening testing for severe combined immunodeficiency. The patient also presented a profound B cell deficiency at birth. METHODS: Genetic, functional, immunologic, and clinical outcome data associated with this patient and her mutation were evaluated. RESULTS: Mutant p.C182* was detected in the cytoplasm of the patient's primary cells, in contrast to wild type (WT) IKAROS protein, only detected in the nucleus. Functional in vitro assessments revealed that p.C182* was less stable than WT IKAROS protein and failed to bind to its target DNA binding sequence and dimerize with WT IKAROS protein, resulting in impaired pericentromeric targeting and transcriptional repression by means of haploinsufficiency. During follow-up, while a spontaneous recovery of TREC and T cells was observed, B cells improved but not to sustained normal ranges. CONCLUSIONS: Patients with IKAROS-associated diseases can present with SCID-like TREC values through newborn screening testing. IKZF1 mutations should be added to the low TREC differential, although spontaneous recovery has to be considered.


Subject(s)
Haploinsufficiency/genetics , Ikaros Transcription Factor/genetics , Mutation/genetics , Severe Combined Immunodeficiency/diagnosis , Severe Combined Immunodeficiency/genetics , B-Lymphocytes/immunology , Common Variable Immunodeficiency/genetics , Common Variable Immunodeficiency/immunology , DNA/genetics , HEK293 Cells , Haploinsufficiency/immunology , Humans , Ikaros Transcription Factor/immunology , Infant, Newborn , Neonatal Screening/methods , Primary Immunodeficiency Diseases/genetics , Primary Immunodeficiency Diseases/immunology , Severe Combined Immunodeficiency/immunology , T-Lymphocytes/immunology
8.
Am J Hum Genet ; 100(4): 676-688, 2017 Apr 06.
Article in English | MEDLINE | ID: mdl-28343629

ABSTRACT

Ubiquitination is a posttranslational modification that regulates many cellular processes including protein degradation, intracellular trafficking, cell signaling, and protein-protein interactions. Deubiquitinating enzymes (DUBs), which reverse the process of ubiquitination, are important regulators of the ubiquitin system. OTUD6B encodes a member of the ovarian tumor domain (OTU)-containing subfamily of deubiquitinating enzymes. Herein, we report biallelic pathogenic variants in OTUD6B in 12 individuals from 6 independent families with an intellectual disability syndrome associated with seizures and dysmorphic features. In subjects with predicted loss-of-function alleles, additional features include global developmental delay, microcephaly, absent speech, hypotonia, growth retardation with prenatal onset, feeding difficulties, structural brain abnormalities, congenital malformations including congenital heart disease, and musculoskeletal features. Homozygous Otud6b knockout mice were subviable, smaller in size, and had congenital heart defects, consistent with the severity of loss-of-function variants in humans. Analysis of peripheral blood mononuclear cells from an affected subject showed reduced incorporation of 19S subunits into 26S proteasomes, decreased chymotrypsin-like activity, and accumulation of ubiquitin-protein conjugates. Our findings suggest a role for OTUD6B in proteasome function, establish that defective OTUD6B function underlies a multisystemic human disorder, and provide additional evidence for the emerging relationship between the ubiquitin system and human disease.


Subject(s)
Abnormalities, Multiple/genetics , Endopeptidases/genetics , Intellectual Disability/genetics , Adolescent , Animals , Child , Child, Preschool , Disease Models, Animal , Female , Gene Deletion , Humans , Male , Mice , Pedigree , Proteasome Endopeptidase Complex/genetics , Proteasome Endopeptidase Complex/metabolism , Seizures/genetics
9.
Hum Mutat ; 40(3): 267-280, 2019 03.
Article in English | MEDLINE | ID: mdl-30520571

ABSTRACT

Next-generation sequencing (NGS) has been instrumental in solving the genetic basis of rare inherited diseases, especially neurodevelopmental syndromes. However, functional workup is essential for precise phenotype definition and to understand the underlying disease mechanisms. Using whole exome (WES) and whole genome sequencing (WGS) in four independent families with hypotonia, neurodevelopmental delay, facial dysmorphism, loss of white matter, and thinning of the corpus callosum, we identified four previously unreported homozygous truncating PPP1R21 alleles: c.347delT p.(Ile116Lysfs*25), c.2170_2171insGGTA p.(Ile724Argfs*8), c.1607dupT p.(Leu536Phefs*7), c.2063delA p.(Lys688Serfs*26) and found that PPP1R21 was absent in fibroblasts of an affected individual, supporting the allele's loss of function effect. PPP1R21 function had not been studied except that a large scale affinity proteomics approach suggested an interaction with PIBF1 defective in Joubert syndrome. Our co-immunoprecipitation studies did not confirm this but in contrast defined the localization of PPP1R21 to the early endosome. Consistent with the subcellular expression pattern and the clinical phenotype exhibiting features of storage diseases, we found patient fibroblasts exhibited a delay in clearance of transferrin-488 while uptake was normal. In summary, we delineate a novel neurodevelopmental syndrome caused by biallelic PPP1R21 loss of function variants, and suggest a role of PPP1R21 within the endosomal sorting process or endosome maturation pathway.


Subject(s)
Alleles , Endocytosis , Loss of Function Mutation/genetics , Neurodevelopmental Disorders/genetics , Neurodevelopmental Disorders/pathology , Phosphoprotein Phosphatases/genetics , Adult , Child , Child, Preschool , Endosomes/metabolism , Endosomes/ultrastructure , Female , Fibroblasts/metabolism , Fibroblasts/ultrastructure , Homozygote , Humans , Infant , Infant, Newborn , Male , Myelin Sheath/metabolism , Myelin Sheath/ultrastructure , Pedigree , Phosphoprotein Phosphatases/chemistry , Syndrome , Transferrin/metabolism
10.
Am J Hum Genet ; 99(3): 720-727, 2016 09 01.
Article in English | MEDLINE | ID: mdl-27545676

ABSTRACT

SON is a key component of the spliceosomal complex and a critical mediator of constitutive and alternative splicing. Additionally, SON has been shown to influence cell-cycle progression, genomic integrity, and maintenance of pluripotency in stem cell populations. The clear functional relevance of SON in coordinating essential cellular processes and its presence in diverse human tissues suggests that intact SON might be crucial for normal growth and development. However, the phenotypic effects of deleterious germline variants in SON have not been clearly defined. Herein, we describe seven unrelated individuals with de novo variants in SON and propose that deleterious variants in SON are associated with a severe multisystem disorder characterized by developmental delay, persistent feeding difficulties, and congenital malformations, including brain anomalies.


Subject(s)
Congenital Abnormalities/genetics , DNA-Binding Proteins/genetics , Developmental Disabilities/genetics , Failure to Thrive/genetics , Intellectual Disability/genetics , Minor Histocompatibility Antigens/genetics , Sequence Deletion/genetics , Adolescent , Brain/abnormalities , Child , Child, Preschool , DNA-Binding Proteins/chemistry , Exome/genetics , Female , Humans , Male , Minor Histocompatibility Antigens/chemistry , Pedigree , Young Adult
11.
PLoS Genet ; 12(4): e1005848, 2016 Apr.
Article in English | MEDLINE | ID: mdl-27120463

ABSTRACT

Genetic leukoencephalopathies (gLEs) are a group of heterogeneous disorders with white matter abnormalities affecting the central nervous system (CNS). The causative mutation in ~50% of gLEs is unknown. Using whole exome sequencing (WES), we identified homozygosity for a missense variant, VPS11: c.2536T>G (p.C846G), as the genetic cause of a leukoencephalopathy syndrome in five individuals from three unrelated Ashkenazi Jewish (AJ) families. All five patients exhibited highly concordant disease progression characterized by infantile onset leukoencephalopathy with brain white matter abnormalities, severe motor impairment, cortical blindness, intellectual disability, and seizures. The carrier frequency of the VPS11: c.2536T>G variant is 1:250 in the AJ population (n = 2,026). VPS11 protein is a core component of HOPS (homotypic fusion and protein sorting) and CORVET (class C core vacuole/endosome tethering) protein complexes involved in membrane trafficking and fusion of the lysosomes and endosomes. The cysteine 846 resides in an evolutionarily conserved cysteine-rich RING-H2 domain in carboxyl terminal regions of VPS11 proteins. Our data shows that the C846G mutation causes aberrant ubiquitination and accelerated turnover of VPS11 protein as well as compromised VPS11-VPS18 complex assembly, suggesting a loss of function in the mutant protein. Reduced VPS11 expression leads to an impaired autophagic activity in human cells. Importantly, zebrafish harboring a vps11 mutation with truncated RING-H2 domain demonstrated a significant reduction in CNS myelination following extensive neuronal death in the hindbrain and midbrain. Thus, our study reveals a defect in VPS11 as the underlying etiology for an autosomal recessive leukoencephalopathy disorder associated with a dysfunctional autophagy-lysosome trafficking pathway.


Subject(s)
Autophagy/genetics , Founder Effect , Genes, Recessive , Leukoencephalopathies/genetics , Mutation , Vesicular Transport Proteins/genetics , Adult , Amino Acid Sequence , Animals , Cell Death/genetics , Child , Child, Preschool , Female , Humans , Infant , Male , Molecular Sequence Data , Sequence Homology, Amino Acid , Vesicular Transport Proteins/chemistry , Young Adult
12.
Genome Res ; 25(3): 305-15, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25637381

ABSTRACT

Recommendations for laboratories to report incidental findings from genomic tests have stimulated interest in such results. In order to investigate the criteria and processes for assigning the pathogenicity of specific variants and to estimate the frequency of such incidental findings in patients of European and African ancestry, we classified potentially actionable pathogenic single-nucleotide variants (SNVs) in all 4300 European- and 2203 African-ancestry participants sequenced by the NHLBI Exome Sequencing Project (ESP). We considered 112 gene-disease pairs selected by an expert panel as associated with medically actionable genetic disorders that may be undiagnosed in adults. The resulting classifications were compared to classifications from other clinical and research genetic testing laboratories, as well as with in silico pathogenicity scores. Among European-ancestry participants, 30 of 4300 (0.7%) had a pathogenic SNV and six (0.1%) had a disruptive variant that was expected to be pathogenic, whereas 52 (1.2%) had likely pathogenic SNVs. For African-ancestry participants, six of 2203 (0.3%) had a pathogenic SNV and six (0.3%) had an expected pathogenic disruptive variant, whereas 13 (0.6%) had likely pathogenic SNVs. Genomic Evolutionary Rate Profiling mammalian conservation score and the Combined Annotation Dependent Depletion summary score of conservation, substitution, regulation, and other evidence were compared across pathogenicity assignments and appear to have utility in variant classification. This work provides a refined estimate of the burden of adult onset, medically actionable incidental findings expected from exome sequencing, highlights challenges in variant classification, and demonstrates the need for a better curated variant interpretation knowledge base.


Subject(s)
Exome , Genomics , Incidental Findings , Adult , Black People/genetics , Female , Gene Frequency , Genes, Dominant , Genetic Association Studies , Genetic Testing , Genome, Human , Genomics/methods , High-Throughput Nucleotide Sequencing , Humans , Male , Phenotype , Polymorphism, Single Nucleotide , White People/genetics
13.
Am J Med Genet A ; 176(7): 1667-1669, 2018 07.
Article in English | MEDLINE | ID: mdl-29740950

ABSTRACT

Pathogenic variants in CHD2 (chromodomain helicase DNA-binding protein 2) have been reported in neurodevelopmental disorders with a broad spectrum of phenotypic variability, ranging from mild intellectual disability to atonic-myoclonic epilepsy. However, given the paucity of reported cases the extent of this phenotypic spectrum is currently unknown. Furthermore, all confirmed pathogenic CHD2 variants reported to date have been de novo, preventing the study of intrafamilial phenotypic heterogeneity and creating ambiguity regarding recurrence risk, penetrance, and expressivity. Here, we report the first known case of an inherited pathogenic CHD2 variant in affected mother and daughter. This case demonstrates intrafamilial phenotypic heterogeneity and confirms potential heritability of CHD2-related neurodevelopmental disorders.


Subject(s)
DNA-Binding Proteins/genetics , Mutation , Neurodevelopmental Disorders/genetics , Neurodevelopmental Disorders/pathology , Adult , Child, Preschool , Electroencephalography , Humans , Middle Aged , Mothers , Nuclear Family , Phenotype , Young Adult
14.
Mol Cell ; 37(3): 333-43, 2010 Feb 12.
Article in English | MEDLINE | ID: mdl-20159553

ABSTRACT

Saccharomyces WEE1 (Swe1), the only "true" tyrosine kinase in budding yeast, is an Hsp90 client protein. Here we show that Swe1(Wee1) phosphorylates a conserved tyrosine residue (Y24 in yeast Hsp90 and Y38 in human Hsp90alpha) in the N domain of Hsp90. Phosphorylation is cell-cycle associated and modulates the ability of Hsp90 to chaperone a selected clientele, including v-Src and several other kinases. Nonphosphorylatable mutants have normal ATPase activity, support yeast viability, and productively chaperone the Hsp90 client glucocorticoid receptor. Deletion of SWE1 in yeast increases Hsp90 binding to its inhibitor geldanamycin, and pharmacologic inhibition/silencing of Wee1 sensitizes cancer cells to Hsp90 inhibitor-induced apoptosis. These findings demonstrate that Hsp90 chaperoning of distinct client proteins is differentially regulated by specific posttranslational modification of a unique subcellular pool of the chaperone, and they provide a strategy to increase the cellular potency of Hsp90 inhibitors.


Subject(s)
Cell Cycle Proteins/physiology , HSP90 Heat-Shock Proteins/metabolism , Protein-Tyrosine Kinases/physiology , Saccharomyces cerevisiae Proteins/physiology , Tyrosine/metabolism , Cell Cycle Proteins/antagonists & inhibitors , Cell Cycle Proteins/genetics , Cell Line, Tumor , Dimerization , HSP90 Heat-Shock Proteins/physiology , Humans , Nuclear Proteins/antagonists & inhibitors , Nuclear Proteins/genetics , Nuclear Proteins/physiology , Phosphorylation , Proteasome Endopeptidase Complex/metabolism , Protein-Tyrosine Kinases/antagonists & inhibitors , Protein-Tyrosine Kinases/genetics , RNA Interference , Saccharomyces cerevisiae Proteins/antagonists & inhibitors , Saccharomyces cerevisiae Proteins/genetics , Ubiquitination
15.
Genet Med ; 19(8): 936-944, 2017 08.
Article in English | MEDLINE | ID: mdl-28125085

ABSTRACT

PURPOSE: To investigate pan-ethnic SMN1 copy-number and sequence variation by hybridization-based target enrichment coupled with massively parallel sequencing or next-generation sequencing (NGS). METHODS: NGS reads aligned to SMN1 and SMN2 exon 7 were quantified to determine the total combined copy number of SMN1 and SMN2. The ratio of SMN1 to SMN2 was calculated based on a single-nucleotide difference that distinguishes the two genes. SMN1 copy-number results were compared between the NGS and quantitative polymerase chain reaction and/or multiplex ligation-dependent probe amplification. The NGS data set was also queried for the g.27134T>G single-nucleotide polymorphism (SNP) and other SMN1 sequence pathogenic variants. RESULTS: The sensitivity of the test to detect spinal muscular atrophy (SMA) carriers with one copy of SMN1 was 100% (95% confidence interval (CI): 95.9-100%; n = 90) and specificity was 99.6% (95% CI: 99.4-99.7%; n = 6,648). Detection of the g.27134T>G SNP by NGS was 100% concordant with an restriction fragment-length polymorphism method (n = 493). Ten single-nucleotide variants in SMN1 were detectable by NGS and confirmed by gene-specific amplicon-based sequencing. This comprehensive approach yielded SMA carrier detection rates of 90.3-95.0% in five ethnic groups studied. CONCLUSION: We have developed a novel, comprehensive SMN1 copy-number and sequence variant analysis method by NGS that demonstrated improved SMA carrier detection rates across the entire population examined.Genet Med advance online publication 19 January 2017.


Subject(s)
Genetic Carrier Screening , High-Throughput Nucleotide Sequencing/methods , Muscular Atrophy, Spinal/genetics , Survival of Motor Neuron 1 Protein/genetics , Gene Dosage , Humans , Muscular Atrophy, Spinal/ethnology , Polymorphism, Single Nucleotide , Reproducibility of Results , Sensitivity and Specificity , Survival of Motor Neuron 2 Protein/genetics
16.
Am J Hum Genet ; 93(4): 631-40, 2013 Oct 03.
Article in English | MEDLINE | ID: mdl-24055113

ABSTRACT

The incorporation of genomics into medicine is stimulating interest on the return of incidental findings (IFs) from exome and genome sequencing. However, no large-scale study has yet estimated the number of expected actionable findings per individual; therefore, we classified actionable pathogenic single-nucleotide variants in 500 European- and 500 African-descent participants randomly selected from the National Heart, Lung, and Blood Institute Exome Sequencing Project. The 1,000 individuals were screened for variants in 114 genes selected by an expert panel for their association with medically actionable genetic conditions possibly undiagnosed in adults. Among the 1,000 participants, 585 instances of 239 unique variants were identified as disease causing in the Human Gene Mutation Database (HGMD). The primary literature supporting the variants' pathogenicity was reviewed. Of the identified IFs, only 16 unique autosomal-dominant variants in 17 individuals were assessed to be pathogenic or likely pathogenic, and one participant had two pathogenic variants for an autosomal-recessive disease. Furthermore, one pathogenic and four likely pathogenic variants not listed as disease causing in HGMD were identified. These data can provide an estimate of the frequency (∼3.4% for European descent and ∼1.2% for African descent) of the high-penetrance actionable pathogenic or likely pathogenic variants in adults. The 23 participants with pathogenic or likely pathogenic variants were disproportionately of European (17) versus African (6) descent. The process of classifying these variants underscores the need for a more comprehensive and diverse centralized resource to provide curated information on pathogenicity for clinical use to minimize health disparities in genomic medicine.


Subject(s)
Disease/genetics , Exome , Genetic Predisposition to Disease , Incidental Findings , Polymorphism, Single Nucleotide , Databases, Genetic , Gene Frequency , Humans , Penetrance
17.
Am J Med Genet A ; 170A(5): 1196-201, 2016 May.
Article in English | MEDLINE | ID: mdl-26789280

ABSTRACT

High quality information is critical for informed decision-making in pregnancy following a prenatal diagnosis of sex chromosome aneuploidy. The goal of this study was to define the spectrum of outcomes in patients with prenatally diagnosed 45,X/46,XX mosaic Turner syndrome in order to provide a better basis for genetic counseling at the time of intrauterine diagnosis. Phenotype data for twenty-five patients with prenatally diagnosed 45,X/46,XX mosaicism were collected by retrospective chart review and, when possible, semi-structured telephone interview. Existing data from a cohort of 58 patients with postnatally diagnosed 45,X/46,XX mosaicism were used for comparison. Relative to those diagnosed postnatally, prenatal patients were more likely to have normal growth and normal secondary sexual development, less likely to manifest distinctive Turner syndrome features such as nuchal webbing and edema, and had significantly fewer renal defects. These differences underscore the need for a nuanced approach to prenatal counseling in cases of 45,X/46,XX mosaicism.


Subject(s)
Aneuploidy , Genetic Counseling , Mosaicism , Turner Syndrome/genetics , Adolescent , Adult , Child , Child, Preschool , Female , Humans , Infant , Karyotyping , Male , Pregnancy , Pregnancy Outcome , Prenatal Diagnosis , Sex Chromosomes/genetics , Turner Syndrome/diagnosis , Turner Syndrome/pathology
18.
Strahlenther Onkol ; 186(1): 36-39, 2010 Jan.
Article in English | MEDLINE | ID: mdl-20082186

ABSTRACT

PURPOSE: To investigate technical feasibilities of noncoplanar proton-beam therapy (PBT) on dose reduction to critical organs. MATERIAL AND METHODS: The degree of mechanical precision, rotational limitations of the gantry and the treatment couch were evaluated, and dose-volume histograms were compared for noncoplanar and coplanar PBT. Following these studies, three patients with tumors proximal to the optic nerve underwent noncoplanar PBT. RESULTS: Noncoplanar PBT offered advantage in dose reduction to the optic nerve when compared to coplanar therapy. This advantage was more significant if the tumor reduced in size during treatment. None experienced radiation injury to the optic nerve during a short follow-up time of 7-12 months. CONCLUSION: Noncoplanar PBT appears to reduce doses to organs at risk.


Subject(s)
Adenoma, Pleomorphic/radiotherapy , Brain Neoplasms/radiotherapy , Eyelid Neoplasms/radiotherapy , Frontal Lobe/radiation effects , Glioblastoma/radiotherapy , Meningeal Neoplasms/radiotherapy , Meningioma/radiotherapy , Optic Nerve/radiation effects , Proton Therapy , Radiation Injuries/prevention & control , Dose Fractionation, Radiation , Female , Humans , Middle Aged , Optic Chiasm/radiation effects , Particle Accelerators , Radiotherapy Dosage , Radiotherapy Planning, Computer-Assisted , Retina/radiation effects , Synchrotrons
19.
Strahlenther Onkol ; 185(12): 782-8, 2009 Dec.
Article in English | MEDLINE | ID: mdl-20013087

ABSTRACT

BACKGROUND AND PURPOSE: The prognosis of patients with advanced hepatocellular carcinoma (HCC) with portal vein tumor thrombosis (PVTT) is extremely poor, as effective treatment options are limited. The authors performed a retrospective review to evaluate the efficacy of proton-beam therapy (PBT) for patients presenting with PVTT in the setting of HCC. PATIENTS AND METHODS: Between February 1991 and September 2005, 35 patients with HCC and tumor thrombi in the main trunk or major branches of the portal vein presented for consideration of PBT. Their tumor sizes ranged from 25 mm to 130 mm (median, 60 mm). A median total dose of 72.6 GyE in 22 fractions was delivered over 31 days to a target volume that encompassed both the primary hepatic lesion and the PVTT. RESULTS: 32 patients were progression-free during a median follow-up period of 21 months (range, 2-88 months) and three patients experienced disease progression. Local progression-free survival rates were 46% at 2 years and 20% at 5 years, and the median local progression-free survival was 21 months. Acute toxicity > or = grade 3 was observed in three patients, and no patient experienced late toxicity > or = grade 3. None of the patients had to discontinue treatment as a result of toxicity. CONCLUSION: PBT improved local control and significantly prolonged survival in HCC patients with PVTT.


Subject(s)
Carcinoma, Hepatocellular/radiotherapy , Liver Neoplasms/radiotherapy , Neoplastic Cells, Circulating/radiation effects , Portal Vein/radiation effects , Proton Therapy , Adult , Aged , Aged, 80 and over , Carcinoma, Hepatocellular/mortality , Carcinoma, Hepatocellular/pathology , Combined Modality Therapy , Disease Progression , Disease-Free Survival , Dose Fractionation, Radiation , Female , Follow-Up Studies , Humans , Liver Neoplasms/mortality , Liver Neoplasms/pathology , Magnetic Resonance Imaging , Male , Middle Aged , Neoplasm Staging , Neoplastic Cells, Circulating/pathology , Prognosis , Radiation Injuries/etiology , Radiotherapy Dosage , Radiotherapy Planning, Computer-Assisted , Radiotherapy, Adjuvant , Retrospective Studies , Tomography, X-Ray Computed , Treatment Outcome
20.
Article in English | MEDLINE | ID: mdl-31196892

ABSTRACT

Neonatal diabetes mellitus (NDM) is a rare condition that presents with diabetes in the first few months of life. The treatment of NDM may differ depending on the genetic etiology, with numerous studies showing the benefit of sulfonylurea therapy in cases caused by mutations in KCNJ11 or ABCC8 Mutations in the insulin gene (INS) have also been identified as causes of NDM; these cases are generally best treated with insulin alone. We report a case of a female infant born small for gestational age (SGA) at late preterm diagnosed with NDM at 7 wk of life who was found by rapid whole-genome sequencing to harbor a novel de novo c.26C>G (p.Pro9Arg) variant in the INS gene. She presented with diabetic ketoacidosis, which responded to insulin therapy. She did not respond to empiric trial of sulfonylurea therapy early in her hospital course, and it was discontinued once a genetic diagnosis was made. Early genetic evaluation in patients presenting with NDM is essential to optimize therapeutic decision-making.


Subject(s)
Diabetes Mellitus/genetics , Infant, Newborn, Diseases/genetics , Insulin/genetics , Diabetic Ketoacidosis/genetics , Female , Humans , Infant, Newborn , Mutation
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