SNP Arrays

Louhelainen, Jari

doi:10.3390/microarrays5040027

Cited by 9 publications

(5 citation statements)

References 9 publications

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“…Single nucleotide polymorphism (SNP) arrays are highthroughput DNA microarrays that originated from the early 2000s and are a powerful platform for simultaneously analyzing hundreds of thousands of SNPs and evaluating CNVs in a single experiment (5). Recently, the cost of SNP arrays has decreased substantially (from 300 Euro to 40 Euros per sample), driven by the very large sample sizes needed to perform genomewide association studies (GWAS).…”

Section: Introductionmentioning

confidence: 99%

Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency

et al. 2020

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Section: Introductionmentioning

confidence: 99%

Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency

et al. 2020

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“…SNP arrays are high-efficiency DNA microarrays that are a robust platform for simultaneously examining hundreds of thousands of SNPs and evaluating CNVs in a single experiment [ 43 ]. Recently, the cost of SNP arrays has decreased appreciably, driven by the very large sample sizes needed to perform genome-wide association studies.…”

Section: Discussionmentioning

confidence: 99%

Compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case report

et al. 2021

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Background Ataxia-telangiectasia is a rare autosomal recessive, neurodegenerative disorder caused by alterations in the ATM gene. The majority of ATM pathogenic variants are frameshift or nonsense variants which are predicted to truncate the whole ATM protein. Herein, we report on an ataxia telangiectasia child with atypical phenotype who was identified as compound heterozygous for two ATM variants involving a previously described pathogenic single nucleotide variation (SNV) and a novel copy number variation (CNV). Case presentation A 6-year-old boy presented with delayed development and oculomotor apraxia. Brain magnetic resonance imaging showed interval development of mild atrophy in the cerebellum. Serum alpha fetoprotein level was in normal range. Next-generation sequencing and single-nucleotide polymorphism array tests were performed. Next-generation sequencing revealed a heterozygous nonsense pathogenic variant in ATM, c.742C > T (p.Arg248Ter) inherited from the father. Single-nucleotide polymorphism array revealed a compound heterozygous CNV, arr[GRCh37] 11q22.3(10851766–108183226) × 1, 31460 bp (exons 24–40 deletion of ATM) inherited from the mother, which was validated by reverse transcription-polymerase chain reaction analysis (RT-PCR). We demonstrated that this variant (NM_000051.4:c.3403_6006del) generated a product of in-frame deletion of exon 24–40 of ATM (p.Ser1135_Gln2002del). Conclusions The compound heterozygosity for ATM variants involving a previously described pathogenic SNV and a novel CNV may be associated with the atypical clinical manifestations. This clinical report extends the genetic and phenotypic spectrum of ATM pathogenic variants in atypical ataxia-telangiectasia, thus making implementation of advanced analysis beyond the routine next-generation sequencing an important consideration in diagnosis and rehabilitation services for children with ataxia-telangiectasia.

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“…This led to a small number of children tested with this technique in our cohort ( 42 ). SNP-array usually detects DNA duplications and deletions ( 44 ), whereas gene panel analysis (mutation analyses in selected genes), and WES can detect specific variants/mutations of which the origin can be identified by including the parents in the analysis ( 45 ). Nowadays, WES is becoming more and more available and costs are reducing.…”

Section: Discussionmentioning

confidence: 99%

Clinical Characteristics and Genetic Etiology of Children With Developmental Language Disorder

et al. 2021

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Objective: Developmental language delay (DLD) is one of the most common disabilities in childhood and can negatively affect a child's communication skills and academic and/or psychosocial development. To date, an increasing number of causative genes have been identified by diagnostic techniques like next generation sequencing. An early genetic diagnosis is important to properly prepare and counsel children and parents for possible future difficulties. Despite this, genetic assessment is usually not part of a standardized diagnostic set in children with developmental language delay. In this study, we aim to assess the diagnostic outcomes of children primarily assessed for speech and language delay who were subsequently referred for genetic etiological assessment.Methods: Medical records of children referred to the department of Otorhinolaryngology of the Wilhelmina Children's Hospital for diagnostic work-up for a suspected speech and language delay between June 2011 and December 2018 who were additionally referred to a geneticist were evaluated. Study parameters concerning medical history, behavioral problems, language development, intelligence, and hearing were recorded. Outcomes of genetic analysis were evaluated.Results: A total of 127 patients were diagnosed with a developmental language delay. Genetic analysis was conducted in 119 out of 127 patients with a language delay and eligible for this study. The median time between initial speech and language assessment and the first genetic consultation was 10 months (IQR 5.0–23.0). In 34 out of 127 patients a causative genetic diagnosis was found to explain their DLD.Conclusion: In approximately a quarter of the patients (26.8%) diagnosed with developmental language delay, a causative genetic diagnosis was confirmed. This demonstrates the opportunity to identify an underlying genetic etiology in children with developmental language delay. However, in order to optimize the diagnostic process and clinical care for these children, two important research gaps need to be addressed. First, research should focus on assessing the clinical impact and effect on treatment outcomes of a genetic diagnosis. Secondly, it is important to recognize for which children genetic testing is most beneficial.

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SNP Arrays

Cited by 9 publications

References 9 publications

Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency

Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency

Compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case report

Clinical Characteristics and Genetic Etiology of Children With Developmental Language Disorder

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