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1.
Nat Rev Genet ; 25(7): 476-499, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38467784

RESUMEN

Short tandem repeats (STRs) are a class of repetitive elements, composed of tandem arrays of 1-6 base pair sequence motifs, that comprise a substantial fraction of the human genome. STR expansions can cause a wide range of neurological and neuromuscular conditions, known as repeat expansion disorders, whose age of onset, severity, penetrance and/or clinical phenotype are influenced by the length of the repeats and their sequence composition. The presence of non-canonical motifs, depending on the type, frequency and position within the repeat tract, can alter clinical outcomes by modifying somatic and intergenerational repeat stability, gene expression and mutant transcript-mediated and/or protein-mediated toxicities. Here, we review the diverse structural conformations of repeat expansions, technological advances for the characterization of changes in sequence composition, their clinical correlations and the impact on disease mechanisms.


Asunto(s)
Repeticiones de Microsatélite , Humanos , Repeticiones de Microsatélite/genética , Expansión de las Repeticiones de ADN/genética , Genoma Humano
2.
Nature ; 613(7942): 96-102, 2023 01.
Artículo en Inglés | MEDLINE | ID: mdl-36517591

RESUMEN

Expansion of a single repetitive DNA sequence, termed a tandem repeat (TR), is known to cause more than 50 diseases1,2. However, repeat expansions are often not explored beyond neurological and neurodegenerative disorders. In some cancers, mutations accumulate in short tracts of TRs, a phenomenon termed microsatellite instability; however, larger repeat expansions have not been systematically analysed in cancer3-8. Here we identified TR expansions in 2,622 cancer genomes spanning 29 cancer types. In seven cancer types, we found 160 recurrent repeat expansions (rREs), most of which (155/160) were subtype specific. We found that rREs were non-uniformly distributed in the genome with enrichment near candidate cis-regulatory elements, suggesting a potential role in gene regulation. One rRE, a GAAA-repeat expansion, located near a regulatory element in the first intron of UGT2B7 was detected in 34% of renal cell carcinoma samples and was validated by long-read DNA sequencing. Moreover, in preliminary experiments, treating cells that harbour this rRE with a GAAA-targeting molecule led to a dose-dependent decrease in cell proliferation. Overall, our results suggest that rREs may be an important but unexplored source of genetic variation in human cancer, and we provide a comprehensive catalogue for further study.


Asunto(s)
Expansión de las Repeticiones de ADN , Genoma Humano , Neoplasias , Humanos , Secuencia de Bases , Expansión de las Repeticiones de ADN/genética , Genoma Humano/genética , Neoplasias/clasificación , Neoplasias/genética , Neoplasias/patología , Análisis de Secuencia de ADN , Regulación de la Expresión Génica , Elementos Reguladores de la Transcripción/genética , Intrones/genética , Carcinoma de Células Renales/genética , Carcinoma de Células Renales/patología , Proliferación Celular/efectos de los fármacos , Reproducibilidad de los Resultados
3.
Am J Hum Genet ; 110(2): 240-250, 2023 02 02.
Artículo en Inglés | MEDLINE | ID: mdl-36669496

RESUMEN

Spinal muscular atrophy, a leading cause of early infant death, is caused by bi-allelic mutations of SMN1. Sequence analysis of SMN1 is challenging due to high sequence similarity with its paralog SMN2. Both genes have variable copy numbers across populations. Furthermore, without pedigree information, it is currently not possible to identify silent carriers (2+0) with two copies of SMN1 on one chromosome and zero copies on the other. We developed Paraphase, an informatics method that identifies full-length SMN1 and SMN2 haplotypes, determines the gene copy numbers, and calls phased variants using long-read PacBio HiFi data. The SMN1 and SMN2 copy-number calls by Paraphase are highly concordant with orthogonal methods (99.2% for SMN1 and 100% for SMN2). We applied Paraphase to 438 samples across 5 ethnic populations to conduct a population-wide haplotype analysis of these highly homologous genes. We identified major SMN1 and SMN2 haplogroups and characterized their co-segregation through pedigree-based analyses. We identified two SMN1 haplotypes that form a common two-copy SMN1 allele in African populations. Testing positive for these two haplotypes in an individual with two copies of SMN1 gives a silent carrier risk of 88.5%, which is significantly higher than the currently used marker (1.7%-3.0%). Extending beyond simple copy-number testing, Paraphase can detect pathogenic variants and enable potential haplotype-based screening of silent carriers through statistical phasing of haplotypes into alleles. Future analysis of larger population data will allow identification of more diverse haplotypes and genetic markers for silent carriers.


Asunto(s)
Atrofia Muscular Espinal , Lactante , Humanos , Atrofia Muscular Espinal/genética , Atrofia Muscular Espinal/diagnóstico , Mutación , Dosificación de Gen , Linaje , Análisis de Secuencia , Proteína 1 para la Supervivencia de la Neurona Motora/genética , Proteína 2 para la Supervivencia de la Neurona Motora/genética
4.
Am J Hum Genet ; 110(1): 105-119, 2023 01 05.
Artículo en Inglés | MEDLINE | ID: mdl-36493768

RESUMEN

Adult-onset cerebellar ataxias are a group of neurodegenerative conditions that challenge both genetic discovery and molecular diagnosis. In this study, we identified an intronic (GAA) repeat expansion in fibroblast growth factor 14 (FGF14). Genetic analysis of 95 Australian individuals with adult-onset ataxia identified four (4.2%) with (GAA)>300 and a further nine individuals with (GAA)>250. PCR and long-read sequence analysis revealed these were pure (GAA) repeats. In comparison, no control subjects had (GAA)>300 and only 2/311 control individuals (0.6%) had a pure (GAA)>250. In a German validation cohort, 9/104 (8.7%) of affected individuals had (GAA)>335 and a further six had (GAA)>250, whereas 10/190 (5.3%) control subjects had (GAA)>250 but none were (GAA)>335. The combined data suggest (GAA)>335 are disease causing and fully penetrant (p = 6.0 × 10-8, OR = 72 [95% CI = 4.3-1,227]), while (GAA)>250 is likely pathogenic with reduced penetrance. Affected individuals had an adult-onset, slowly progressive cerebellar ataxia with variable features including vestibular impairment, hyper-reflexia, and autonomic dysfunction. A negative correlation between age at onset and repeat length was observed (R2 = 0.44, p = 0.00045, slope = -0.12) and identification of a shared haplotype in a minority of individuals suggests that the expansion can be inherited or generated de novo during meiotic division. This study demonstrates the power of genome sequencing and advanced bioinformatic tools to identify novel repeat expansions via model-free, genome-wide analysis and identifies SCA50/ATX-FGF14 as a frequent cause of adult-onset ataxia.


Asunto(s)
Ataxia Cerebelosa , Factores de Crecimiento de Fibroblastos , Ataxia de Friedreich , Expansión de Repetición de Trinucleótido , Adulto , Humanos , Ataxia/genética , Australia , Ataxia Cerebelosa/genética , Ataxia de Friedreich/genética , Expansión de Repetición de Trinucleótido/genética
5.
Nature ; 586(7828): 292-298, 2020 10.
Artículo en Inglés | MEDLINE | ID: mdl-32999459

RESUMEN

The RecQ DNA helicase WRN is a synthetic lethal target for cancer cells with microsatellite instability (MSI), a form of genetic hypermutability that arises from impaired mismatch repair1-4. Depletion of WRN induces widespread DNA double-strand breaks in MSI cells, leading to cell cycle arrest and/or apoptosis. However, the mechanism by which WRN protects MSI-associated cancers from double-strand breaks remains unclear. Here we show that TA-dinucleotide repeats are highly unstable in MSI cells and undergo large-scale expansions, distinct from previously described insertion or deletion mutations of a few nucleotides5. Expanded TA repeats form non-B DNA secondary structures that stall replication forks, activate the ATR checkpoint kinase, and require unwinding by the WRN helicase. In the absence of WRN, the expanded TA-dinucleotide repeats are susceptible to cleavage by the MUS81 nuclease, leading to massive chromosome shattering. These findings identify a distinct biomarker that underlies the synthetic lethal dependence on WRN, and support the development of therapeutic agents that target WRN for MSI-associated cancers.


Asunto(s)
Roturas del ADN de Doble Cadena , Expansión de las Repeticiones de ADN/genética , Repeticiones de Dinucleótido/genética , Neoplasias/genética , Helicasa del Síndrome de Werner/metabolismo , Proteínas de la Ataxia Telangiectasia Mutada/metabolismo , Línea Celular Tumoral , Cromosomas Humanos/genética , Cromosomas Humanos/metabolismo , Cromotripsis , División del ADN , Replicación del ADN , Proteínas de Unión al ADN/metabolismo , Endodesoxirribonucleasas/metabolismo , Endonucleasas/metabolismo , Inestabilidad Genómica , Humanos , Recombinasas/metabolismo
6.
Nature ; 586(7827): 80-86, 2020 10.
Artículo en Inglés | MEDLINE | ID: mdl-32717741

RESUMEN

Tandem DNA repeats vary in the size and sequence of each unit (motif). When expanded, these tandem DNA repeats have been associated with more than 40 monogenic disorders1. Their involvement in disorders with complex genetics is largely unknown, as is the extent of their heterogeneity. Here we investigated the genome-wide characteristics of tandem repeats that had motifs with a length of 2-20 base pairs in 17,231 genomes of families containing individuals with autism spectrum disorder (ASD)2,3 and population control individuals4. We found extensive polymorphism in the size and sequence of motifs. Many of the tandem repeat loci that we detected correlated with cytogenetic fragile sites. At 2,588 loci, gene-associated expansions of tandem repeats that were rare among population control individuals were significantly more prevalent among individuals with ASD than their siblings without ASD, particularly in exons and near splice junctions, and in genes related to the development of the nervous system and cardiovascular system or muscle. Rare tandem repeat expansions had a prevalence of 23.3% in children with ASD compared with 20.7% in children without ASD, which suggests that tandem repeat expansions make a collective contribution to the risk of ASD of 2.6%. These rare tandem repeat expansions included previously undescribed ASD-linked expansions in DMPK and FXN, which are associated with neuromuscular conditions, and in previously unknown loci such as FGF14 and CACNB1. Rare tandem repeat expansions were associated with lower IQ and adaptive ability. Our results show that tandem DNA repeat expansions contribute strongly to the genetic aetiology and phenotypic complexity of ASD.


Asunto(s)
Trastorno del Espectro Autista/genética , Expansión de las Repeticiones de ADN/genética , Genoma Humano/genética , Genómica , Secuencias Repetidas en Tándem/genética , Femenino , Factores de Crecimiento de Fibroblastos/genética , Predisposición Genética a la Enfermedad , Humanos , Inteligencia/genética , Proteínas de Unión a Hierro/genética , Masculino , Proteína Quinasa de Distrofia Miotónica/genética , Motivos de Nucleótidos , Polimorfismo Genético , Frataxina
7.
Bioinformatics ; 40(2)2024 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-38269623

RESUMEN

MOTIVATION: In diploid organisms, phasing is the problem of assigning the alleles at heterozygous variants to one of two haplotypes. Reads from PacBio HiFi sequencing provide long, accurate observations that can be used as the basis for both calling and phasing variants. HiFi reads also excel at calling larger classes of variation, such as structural or tandem repeat variants. However, current phasing tools typically only phase small variants, leaving larger variants unphased. RESULTS: We developed HiPhase, a tool that jointly phases SNVs, indels, structural, and tandem repeat variants. The main benefits of HiPhase are (i) dual mode allele assignment for detecting large variants, (ii) a novel application of the A*-algorithm to phasing, and (iii) logic allowing phase blocks to span breaks caused by alignment issues around reference gaps and homozygous deletions. In our assessment, HiPhase produced an average phase block NG50 of 480 kb with 929 switchflip errors and fully phased 93.8% of genes, improving over the current state of the art. Additionally, HiPhase jointly phases SNVs, indels, structural, and tandem repeat variants and includes innate multi-threading, statistics gathering, and concurrent phased alignment output generation. AVAILABILITY AND IMPLEMENTATION: HiPhase is available as source code and a pre-compiled Linux binary with a user guide at https://github.com/PacificBiosciences/HiPhase.


Asunto(s)
Genoma Humano , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Análisis de Secuencia de ADN , Algoritmos , Haplotipos , Secuencias Repetidas en Tándem
8.
Am J Hum Genet ; 104(6): 1116-1126, 2019 06 06.
Artículo en Inglés | MEDLINE | ID: mdl-31104771

RESUMEN

Huntington disease (HD) is caused by a CAG repeat expansion in the huntingtin (HTT) gene. Although the length of this repeat is inversely correlated with age of onset (AOO), it does not fully explain the variability in AOO. We assessed the sequence downstream of the CAG repeat in HTT [reference: (CAG)n-CAA-CAG], since variants within this region have been previously described, but no study of AOO has been performed. These analyses identified a variant that results in complete loss of interrupting (LOI) adenine nucleotides in this region [(CAG)n-CAG-CAG]. Analysis of multiple HD pedigrees showed that this LOI variant is associated with dramatically earlier AOO (average of 25 years) despite the same polyglutamine length as in individuals with the interrupting penultimate CAA codon. This LOI allele is particularly frequent in persons with reduced penetrance alleles who manifest with HD and increases the likelihood of presenting clinically with HD with a CAG of 36-39 repeats. Further, we show that the LOI variant is associated with increased somatic repeat instability, highlighting this as a significant driver of this effect. These findings indicate that the number of uninterrupted CAG repeats, which is lengthened by the LOI, is the most significant contributor to AOO of HD and is more significant than polyglutamine length, which is not altered in these individuals. In addition, we identified another variant in this region, where the CAA-CAG sequence is duplicated, which was associated with later AOO. Identification of these cis-acting modifiers have potentially important implications for genetic counselling in HD-affected families.


Asunto(s)
Codón/genética , Enfermedad de Huntington/genética , Enfermedad de Huntington/patología , Péptidos/genética , Expansión de Repetición de Trinucleótido/genética , Adolescente , Adulto , Edad de Inicio , Niño , Femenino , Humanos , Masculino , Persona de Mediana Edad , Linaje
9.
Am J Hum Genet ; 105(1): 151-165, 2019 07 03.
Artículo en Inglés | MEDLINE | ID: mdl-31230722

RESUMEN

Genomic technologies such as next-generation sequencing (NGS) are revolutionizing molecular diagnostics and clinical medicine. However, these approaches have proven inefficient at identifying pathogenic repeat expansions. Here, we apply a collection of bioinformatics tools that can be utilized to identify either known or novel expanded repeat sequences in NGS data. We performed genetic studies of a cohort of 35 individuals from 22 families with a clinical diagnosis of cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS). Analysis of whole-genome sequence (WGS) data with five independent algorithms identified a recessively inherited intronic repeat expansion [(AAGGG)exp] in the gene encoding Replication Factor C1 (RFC1). This motif, not reported in the reference sequence, localized to an Alu element and replaced the reference (AAAAG)11 short tandem repeat. Genetic analyses confirmed the pathogenic expansion in 18 of 22 CANVAS-affected families and identified a core ancestral haplotype, estimated to have arisen in Europe more than twenty-five thousand years ago. WGS of the four RFC1-negative CANVAS-affected families identified plausible variants in three, with genomic re-diagnosis of SCA3, spastic ataxia of the Charlevoix-Saguenay type, and SCA45. This study identified the genetic basis of CANVAS and demonstrated that these improved bioinformatics tools increase the diagnostic utility of WGS to determine the genetic basis of a heterogeneous group of clinically overlapping neurogenetic disorders.


Asunto(s)
Ataxia Cerebelosa/etiología , Biología Computacional/métodos , Intrones , Repeticiones de Microsatélite , Polineuropatías/etiología , Proteína de Replicación C/genética , Trastornos de la Sensación/etiología , Enfermedades Vestibulares/etiología , Algoritmos , Ataxia Cerebelosa/patología , Estudios de Cohortes , Familia , Femenino , Genómica , Humanos , Masculino , Persona de Mediana Edad , Polineuropatías/patología , Trastornos de la Sensación/patología , Síndrome , Enfermedades Vestibulares/patología , Secuenciación Completa del Genoma
10.
N Engl J Med ; 380(15): 1433-1441, 2019 04 11.
Artículo en Inglés | MEDLINE | ID: mdl-30970188

RESUMEN

We report an inborn error of metabolism caused by an expansion of a GCA-repeat tract in the 5' untranslated region of the gene encoding glutaminase (GLS) that was identified through detailed clinical and biochemical phenotyping, combined with whole-genome sequencing. The expansion was observed in three unrelated patients who presented with an early-onset delay in overall development, progressive ataxia, and elevated levels of glutamine. In addition to ataxia, one patient also showed cerebellar atrophy. The expansion was associated with a relative deficiency of GLS messenger RNA transcribed from the expanded allele, which probably resulted from repeat-mediated chromatin changes upstream of the GLS repeat. Our discovery underscores the importance of careful examination of regions of the genome that are typically excluded from or poorly captured by exome sequencing.


Asunto(s)
Errores Innatos del Metabolismo de los Aminoácidos/genética , Ataxia/genética , Discapacidades del Desarrollo/genética , Glutaminasa/deficiencia , Glutaminasa/genética , Glutamina/metabolismo , Repeticiones de Microsatélite , Mutación , Atrofia/genética , Cerebelo/patología , Preescolar , Femenino , Genotipo , Glutamina/análisis , Humanos , Masculino , Fenotipo , Reacción en Cadena de la Polimerasa , Secuenciación Completa del Genoma
11.
Ann Neurol ; 89(4): 686-697, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33389754

RESUMEN

OBJECTIVE: The role of the survival of motor neuron (SMN) gene in amyotrophic lateral sclerosis (ALS) is unclear, with several conflicting reports. A decisive result on this topic is needed, given that treatment options are available now for SMN deficiency. METHODS: In this largest multicenter case control study to evaluate the effect of SMN1 and SMN2 copy numbers in ALS, we used whole genome sequencing data from Project MinE data freeze 2. SMN copy numbers of 6,375 patients with ALS and 2,412 controls were called from whole genome sequencing data, and the reliability of the calls was tested with multiplex ligation-dependent probe amplification data. RESULTS: The copy number distribution of SMN1 and SMN2 between cases and controls did not show any statistical differences (binomial multivariate logistic regression SMN1 p = 0.54 and SMN2 p = 0.49). In addition, the copy number of SMN did not associate with patient survival (Royston-Parmar; SMN1 p = 0.78 and SMN2 p = 0.23) or age at onset (Royston-Parmar; SMN1 p = 0.75 and SMN2 p = 0.63). INTERPRETATION: In our well-powered study, there was no association of SMN1 or SMN2 copy numbers with the risk of ALS or ALS disease severity. This suggests that changing SMN protein levels in the physiological range may not modify ALS disease course. This is an important finding in the light of emerging therapies targeted at SMN deficiencies. ANN NEUROL 2021;89:686-697.


Asunto(s)
Esclerosis Amiotrófica Lateral/genética , Esclerosis Amiotrófica Lateral/patología , Proteína 1 para la Supervivencia de la Neurona Motora/genética , Estudios de Casos y Controles , Estudios de Cohortes , Femenino , Dosificación de Gen , Humanos , Masculino , Reproducibilidad de los Resultados , Factores de Riesgo , Índice de Severidad de la Enfermedad , Proteína 2 para la Supervivencia de la Neurona Motora/genética , Secuenciación Completa del Genoma
13.
Pharmacogenomics J ; 21(2): 251-261, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33462347

RESUMEN

Responsible for the metabolism of ~21% of clinically used drugs, CYP2D6 is a critical component of personalized medicine initiatives. Genotyping CYP2D6 is challenging due to sequence similarity with its pseudogene paralog CYP2D7 and a high number and variety of common structural variants (SVs). Here we describe a novel bioinformatics method, Cyrius, that accurately genotypes CYP2D6 using whole-genome sequencing (WGS) data. We show that Cyrius has superior performance (96.5% concordance with truth genotypes) compared to existing methods (84-86.8%). After implementing the improvements identified from the comparison against the truth data, Cyrius's accuracy has since been improved to 99.3%. Using Cyrius, we built a haplotype frequency database from 2504 ethnically diverse samples and estimate that SV-containing star alleles are more frequent than previously reported. Cyrius will be an important tool to incorporate pharmacogenomics in WGS-based precision medicine initiatives.


Asunto(s)
Citocromo P-450 CYP2D6/genética , Técnicas de Genotipaje/métodos , Alelos , Biología Computacional/métodos , Etnicidad/genética , Genotipo , Haplotipos/genética , Humanos , Polimorfismo Genético/genética , Secuenciación Completa del Genoma/métodos
14.
Mov Disord ; 36(6): 1456-1460, 2021 06.
Artículo en Inglés | MEDLINE | ID: mdl-34008887

RESUMEN

BACKGROUND: GBA mutations are a common risk factor for Parkinson's disease (PD). A recent study has suggested that GBA haplotypes, identified by intronic variants, can affect age at diagnosis of PD. OBJECTIVES: In this study, we assess this hypothesis using long reads across a large cohort and the publicly available Accelerating Medicines Partnership-Parkinson's Disease (AMP-PD) cohort. METHODS: We recruited a PD cohort through the Remote Assessment of Parkinsonism Supporting Ongoing Development of Interventions in Gaucher Disease study (RAPSODI) and sequenced GBA using Oxford Nanopore technology. Genetic and clinical data on the full AMP-PD cohort were obtained from the online portal of the consortium. RESULTS: A total of 1417 participants were analyzed. There was no significant difference in age at PD diagnosis between the two main haplotypes of the GBA gene. CONCLUSIONS: GBA haplotypes do not affect age at diagnosis of PD in the two independent cohorts studied. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.


Asunto(s)
Glucosilceramidasa/genética , Enfermedad de Parkinson , Haplotipos , Humanos , Intrones , Mutación/genética , Enfermedad de Parkinson/diagnóstico , Enfermedad de Parkinson/genética
15.
Genome Res ; 27(1): 157-164, 2017 01.
Artículo en Inglés | MEDLINE | ID: mdl-27903644

RESUMEN

Improvement of variant calling in next-generation sequence data requires a comprehensive, genome-wide catalog of high-confidence variants called in a set of genomes for use as a benchmark. We generated deep, whole-genome sequence data of 17 individuals in a three-generation pedigree and called variants in each genome using a range of currently available algorithms. We used haplotype transmission information to create a phased "Platinum" variant catalog of 4.7 million single-nucleotide variants (SNVs) plus 0.7 million small (1-50 bp) insertions and deletions (indels) that are consistent with the pattern of inheritance in the parents and 11 children of this pedigree. Platinum genotypes are highly concordant with the current catalog of the National Institute of Standards and Technology for both SNVs (>99.99%) and indels (99.92%) and add a validated truth catalog that has 26% more SNVs and 45% more indels. Analysis of 334,652 SNVs that were consistent between informatics pipelines yet inconsistent with haplotype transmission ("nonplatinum") revealed that the majority of these variants are de novo and cell-line mutations or reside within previously unidentified duplications and deletions. The reference materials from this study are a resource for objective assessment of the accuracy of variant calls throughout genomes.


Asunto(s)
Genoma Humano/genética , Genómica , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Análisis de Secuencia de ADN/métodos , Algoritmos , Bases de Datos Genéticas , Exoma/genética , Genotipo , Humanos , Mutación INDEL/genética , Linaje , Polimorfismo de Nucleótido Simple , Programas Informáticos
16.
Genome Res ; 27(11): 1895-1903, 2017 11.
Artículo en Inglés | MEDLINE | ID: mdl-28887402

RESUMEN

Identifying large expansions of short tandem repeats (STRs), such as those that cause amyotrophic lateral sclerosis (ALS) and fragile X syndrome, is challenging for short-read whole-genome sequencing (WGS) data. A solution to this problem is an important step toward integrating WGS into precision medicine. We developed a software tool called ExpansionHunter that, using PCR-free WGS short-read data, can genotype repeats at the locus of interest, even if the expanded repeat is larger than the read length. We applied our algorithm to WGS data from 3001 ALS patients who have been tested for the presence of the C9orf72 repeat expansion with repeat-primed PCR (RP-PCR). Compared against this truth data, ExpansionHunter correctly classified all (212/212, 95% CI [0.98, 1.00]) of the expanded samples as either expansions (208) or potential expansions (4). Additionally, 99.9% (2786/2789, 95% CI [0.997, 1.00]) of the wild-type samples were correctly classified as wild type by this method with the remaining three samples identified as possible expansions. We further applied our algorithm to a set of 152 samples in which every sample had one of eight different pathogenic repeat expansions, including those associated with fragile X syndrome, Friedreich's ataxia, and Huntington's disease, and correctly flagged all but one of the known repeat expansions. Thus, ExpansionHunter can be used to accurately detect known pathogenic repeat expansions and provides researchers with a tool that can be used to identify new pathogenic repeat expansions.


Asunto(s)
Esclerosis Amiotrófica Lateral/genética , Expansión de las Repeticiones de ADN , Secuenciación Completa del Genoma/métodos , Algoritmos , Proteína C9orf72/genética , Bases de Datos Genéticas , Humanos , Medicina de Precisión , Sensibilidad y Especificidad , Programas Informáticos
17.
Bioinformatics ; 35(22): 4754-4756, 2019 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-31134279

RESUMEN

SUMMARY: We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci. AVAILABILITY AND IMPLEMENTATION: ExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Repeticiones de Microsatélite , Programas Informáticos , Genotipo
18.
Genet Med ; 22(5): 945-953, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-32066871

RESUMEN

PURPOSE: Spinal muscular atrophy (SMA), caused by loss of the SMN1 gene, is a leading cause of early childhood death. Due to the near identical sequences of SMN1 and SMN2, analysis of this region is challenging. Population-wide SMA screening to quantify the SMN1 copy number (CN) is recommended by the American College of Medical Genetics and Genomics. METHODS: We developed a method that accurately identifies the CN of SMN1 and SMN2 using genome sequencing (GS) data by analyzing read depth and eight informative reference genome differences between SMN1/2. RESULTS: We characterized SMN1/2 in 12,747 genomes, identified 1568 samples with SMN1 gains or losses and 6615 samples with SMN2 gains or losses, and calculated a pan-ethnic carrier frequency of 2%, consistent with previous studies. Additionally, 99.8% of our SMN1 and 99.7% of SMN2 CN calls agreed with orthogonal methods, with a recall of 100% for SMA and 97.8% for carriers, and a precision of 100% for both SMA and carriers. CONCLUSION: This SMN copy-number caller can be used to identify both carrier and affected status of SMA, enabling SMA testing to be offered as a comprehensive test in neonatal care and an accurate carrier screening tool in GS sequencing projects.


Asunto(s)
Atrofia Muscular Espinal , Secuencia de Bases , Niño , Preescolar , Humanos , Atrofia Muscular Espinal/diagnóstico , Atrofia Muscular Espinal/genética , Proteína 1 para la Supervivencia de la Neurona Motora/genética
19.
Genet Med ; 21(5): 1121-1130, 2019 05.
Artículo en Inglés | MEDLINE | ID: mdl-30293986

RESUMEN

PURPOSE: Current diagnostic testing for genetic disorders involves serial use of specialized assays spanning multiple technologies. In principle, genome sequencing (GS) can detect all genomic pathogenic variant types on a single platform. Here we evaluate copy-number variant (CNV) calling as part of a clinically accredited GS test. METHODS: We performed analytical validation of CNV calling on 17 reference samples, compared the sensitivity of GS-based variants with those from a clinical microarray, and set a bound on precision using orthogonal technologies. We developed a protocol for family-based analysis of GS-based CNV calls, and deployed this across a clinical cohort of 79 rare and undiagnosed cases. RESULTS: We found that CNV calls from GS are at least as sensitive as those from microarrays, while only creating a modest increase in the number of variants interpreted (~10 CNVs per case). We identified clinically significant CNVs in 15% of the first 79 cases analyzed, all of which were confirmed by an orthogonal approach. The pipeline also enabled discovery of a uniparental disomy (UPD) and a 50% mosaic trisomy 14. Directed analysis of select CNVs enabled breakpoint level resolution of genomic rearrangements and phasing of de novo CNVs. CONCLUSION: Robust identification of CNVs by GS is possible within a clinical testing environment.


Asunto(s)
Variaciones en el Número de Copia de ADN/genética , Enfermedades Raras/genética , Enfermedades no Diagnosticadas/genética , Adolescente , Niño , Preescolar , Mapeo Cromosómico/métodos , Estudios de Cohortes , Femenino , Pruebas Genéticas/métodos , Genoma Humano , Genómica/métodos , Humanos , Lactante , Masculino , Enfermedades Raras/diagnóstico , Enfermedades no Diagnosticadas/diagnóstico , Secuenciación Completa del Genoma/métodos , Adulto Joven
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