A labor- and cost-effective non-optical semiconductor (Ion Torrent) next-generation sequencing of the SLC12A3 and CLCNKA/B genes in Gitelman’s syndrome patients

Liu

et al. 2017

JNS

OBJECTIVE Moyamoya disease (MMD) is a rare, genetically heterogeneous cerebrovascular disease. The authors conducted a genetic study of really interesting new gene (RING) finger protein 213 ( RNF213); actin alpha 2 ( ACTA2); BRCA1/BRCA2-containing complex subunit 3 ( BRCC3); and guanylate cyclase 1, soluble, alpha 3 ( GUCY1A3) as well as a clinical phenotype analysis in Chinese MMD patients to determine whether genetic differences are responsible for the different clinical features that appear in MMD in different ethnicities. METHODS A panel was designed to identify disease-causing mutations in MMD genes and those involved in related disorders ( RNF213, ACTA2, BRCC3, and GUCY1A3). The panel was used to detect disease-causing mutations in 255 Chinese MMD patients. Genotype and allele frequencies were compared between patients and 300 controls. A mutation segregation analysis was performed in 34 families, and genotype-phenotype correlations were made. RESULTS Twenty-seven rare missense variants of RNF213 were identified and were not found in controls. Among them, p.R4810K was identified in 31.4% of patients (80 of 255) with MMD. Significantly higher frequencies of the A allele and G/A genotype of p.R4810K were observed in MMD patients compared with controls (χ = 104.166, p < 0.000). Twenty-five rare variants were identified in 10.6% of patients (27 of 255) without p.R4810K variants. Segregation analysis supported an association between MMD and 3 variants. No possible disease-causing mutations were identified in ACTA2, BRCC3, or GUCY1A3. Compared with patients without the rare variants in RNF213, the p.R4810K heterozygous patients were younger at diagnosis (25 vs 29 years old, p = 0.049) and had more familial cases (24% vs 4.4%, p = 0.000), ischemic cases (81.3% vs 67.5%, p = 0.037), and involvement of the posterior cerebral artery (52% vs 32.5%, p = 0.007). CONCLUSIONS RNF213 is the major susceptibility gene in Chinese MMD patients. The spectrum of rare variants identified in Chinese MMD patients was diverse. Compared to patients without the rare variants in RNF213, the p.R4810K heterozygous patients exhibited different clinical features.

Section: Discussionmentioning

confidence: 99%

Section: Dna Sequencing and Data Analysismentioning

confidence: 99%

RNF213 as the major susceptibility gene for Chinese patients with moyamoya disease and its clinical relevance

Liu

et al. 2017

JNS

Clinical Chemistry and Laboratory Medicine (CCLM)

“…We had previously demonstrated that this pooling approach is valid to identify rare variants that are diluted by the common allele [11,12] . The DNA from each patient was obtained from blood leukocytes and adjusted to 10 ng/ μ L using the Real Time Taqman quantifi cation with RNase P (Life Technologies).…”

Section: Ngs Of Abcb1mentioning

confidence: 98%

ABCB1 (MDR-1) pharmacogenetics of tacrolimus in renal transplanted patients: a Next Generation Sequencing approach

Tavira¹,

Gómez²,

Díaz‐Corte³

et al. 2015

Self Cite

“…The experimental procedure was reported elsewhere Tavira et al 2014), and full details are available upon request to the corresponding author. A twotube multiplex amplification for the coding sequence exons plus at least five intronic flanking nucleotides of NOTCH3 and HTRA1 was designated online (Ion AmpliSeq™ Designer v3.4; https://www.ampliseq.com).…”

Section: Next-generation Sequencingmentioning

confidence: 99%

A Next-Generation Sequencing of the NOTCH3 and HTRA1 Genes in CADASIL Patients

et al. 2015

Self Cite

Our purpose was to develop a next-generation sequencing procedure to search for NOTCH3 and HTRA1 mutations in patients with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) features. A total of 70 patients were sequenced with semiconductor chips in an Ion Torrent Personal Genome Machine. The putative mutations were confirmed through Sanger sequencing of the corresponding patient. Six patients had a typical cysteine-involving NOTCH3 mutation. A new non-reported NOTCH3 variant (p.Pro2178Ser) was found in two patients. One patient was heterozygous for a non-reported HTRA1 variant, likely non-pathogenic (p.Ser139Ala). We found a typical NOTCH3 mutation in 9 % of the patients. None of the patients had HTRA1 variants with likely pathogenic effect. The next-generation sequencing (NGS) procedure here described would facilitate the rapid and cost-effective screening of large cohorts of CADASIL patients.