Identification of a novel frameshift mutation in PAX6 gene and the clinical management in an Asian Indian aniridia family

Purpose: This study aimed to characterize an Asian Indian aniridia family for both the phenotype and genotype of the disease for a better clinical management. Methods: The phenotype and genotype of the affected and unaffected individuals in the aniridia family were evaluated. The subjects underwent a standard ophthalmic evaluation followed by molecular screening of PAX6 gene in the peripheral blood for mutation detection. Results: The three affected individuals had aniridia with several common features and an uncommon presentation of bilateral congenital ptosis. Two affected siblings, a brother and a sister, had aniridia, nystagmus, ptosis, increase in central corneal thickness, cataract, and foveal hypoplasia. The sister had features of glaucoma. The offspring of the sister had all the features except cataract and rise in intraocular pressure. Mutation screening of PAX6 gene helped in identifying a novel heterozygous pathogenic variation g. 31801757dupG (c. 216-19dupG) that resulted in a frameshift mutation that extended into exon 7. Based on the evaluation and diagnostic testing, the family was clinically managed along with genetic counselling. Conclusion: Molecular diagnostic testing helps in genetic counseling of the family with aniridia to understand the nature of the disease and detection of complications early for better management.

High-resolution melting-based TILLING of γ ray-induced mutations in rice / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics strategy for the high-throughput screening of induced mutations. γ radiation, which often induces both insertion/deletion (Indel) and point mutations, has been widely used in mutation induction and crop breeding. The present study aimed to develop a simple, high-throughput TILLING system for screening γ ray-induced mutations using high-resolution melting (HRM) analysis. Pooled rice (Oryza sativa) samples mixed at a 1:7 ratio of Indel mutant to wild-type DNA could be distinguished from the wild-type controls by HRM analysis. Thus, an HRM-TILLING system that analyzes pooled samples of four M2 plants is recommended for screening γ ray-induced mutants in rice. For demonstration, a γ ray-mutagenized M2 rice population (n=4560) was screened for mutations in two genes, OsLCT1 and SPDT, using this HRM-TILLING system. Mutations including one single nucleotide substitution (G→A) and one single nucleotide insertion (A) were identified in OsLCT1, and one trinucleotide (TTC) deletion was identified in SPDT. These mutants can be used in rice breeding and genetic studies, and the findings are of importance for the application of γ ray mutagenesis to the breeding of rice and other seed crops.

Mutation analysis of NPHS2 in Chinese Han adult-onset focal segmental glomerulosclerosis / 上海交通大学学报（医学版）

Objective·To screen NPHS2 mutations in adult focal segmental glomerulosclerosis(FSGS)patients based on a large Chinese FSGS cohort. Methods · All patients were biopsy determined FSGS by the Department of Nephrology at Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine. FSGS secondary to systemic disease and other hereditary kidney disease were excluded. After extraction of genomic DNA of peripheral blood,NPHS2 was screened by directly sequencing the exon/intron junction or high-throughput sequencing,including whole exon sequencing and Panel sequencing, and then verified by Sanger sequencing. One hundred healthy controls were enrolled to validate candidate mutations. Results · Two hundred and four FSGS patients were enrolled,including 52 familial(25.5%) and 152 sporadic patients(74.5%),of which steroid-resistant FSGS patients accounted for 30.3%(46/152).By sequencing NPHS2 in all patients of the cohort(Sanger sequencing in 61 patients and high-throughput sequencing in 143 patients), 2 novel conserved mutations were identified, one homozygous mutation in sporadic steroid-resistant FSGS, p.N199I and one heterozygous mutation in familial FSGS, p.L321fx346. Both of them were not detected in 100 healthy controls. These two variants were predicted to be damaging by Polyphen,SIFT and Mutation Taster.Totally,the mutation rate of NPHS2 in the FSGS cohort was 1%. Conclusion·Since the overall frequency of NPHS2 mutations is considerably low in Chinese adult-onset FSGS,NPHS2 is not the main disease-causing gene of this group of people.

Application of gene chip joint pyrosequencing technology in the newborn genetic deafness gene mutation screening / 中国耳鼻咽喉头颈外科

OBJECTIVE To study the gene chip joint pyrosequencing technology in the newborn genetic deafness gene mutation screening, and provide a theoretical basis for the early diagnosis and prevention of genetic deafness. METHODS 2000 Neonatal EDTA umbilical cord blood was collected and genomic DNA (gDNA) was extracted. Microarray chip was used to detect four deafness gene at 9 mutation sites. And the positive result of gene chip detection was verified by pyrosequencing.RESULTS Among the GJB2 mutations, there were 1 case of 35delG mutation type, 3 cases of 176 del16 mutation type, 57 cases of 235del C mutation type, 9 cases of 299 del AT mutation type, 6 cases of GJB3 gene 538C>T mutation type. There were 5 cases of 1555A>G mutations and 1 case of 1494C>T mutations in mitochondrial 12S rRNA. There were 6 cases of 2168A>G mutation type and 23 cases of IVS7-2A>G mutations in SLC26A4. 103 cases of newborns carry the mutated gene in 2,000, the gene mutation rate is 5.15%. CONCLUSION All the four genes mutation at nine mutation sites are found in newborns with family history of non-hereditary deafness, and GJB2 gene mutation is common. The screening of genetic deafness in newborns is very important for early diagnosis and prevention of hereditary hearing loss. In particular, the diagnosis of mitochondrial 12S rRNA gene mutation can prevent the occurrence of deafness caused by drug use, for the genetic mutation of these carriers' health is of great significance.

Mutation analysis of Pax6 in Chinese patients with congenital aniridia / 中华实验眼科杂志

Background Congenital aniridia is a rare congenital autosomal dominant disease,which is shown as aniridia of double eyes,and the paired box gene 6 (Pax6) gene mutation is now known to be associated with congenital aniridia.Objective This study was to screen the Pax6 gene mutation in patients with congenital aniridia.Methods Eleven patients with congenital aniridia were enrolled in Tianjin Eye Hospital from August 2012 to October 2015,including 6 patients from 3 congenital aniridia family and 5 sporadic patients.All patients received routine ophthalmic examination.Peripheral venous blood of 3 ml was collected from the patients for DNA extraction according to the standard process of DNA isolation instructions,and all the exons of Pax6 gene,Elp4 gene,exon 5 ' and 3',intron splice sequence and SIMO sequence were amplified by PCR.Pax6 genes of the patients were sequenced using Sanger direct sequencing and multiplex ligation dependent probe amplification (MLPA) and compared with those of 500 ocular trauma patients.This study complied with Helsinki declaration,and written informed consent was obtained from each patient prior to any medical examination.Results Iris absence was found in all the patients,and the visions acuity was hand motion to 0.2.Lens dislocation was seen in 1 patient.Direct sequencing results found that three patients in AN-O1 family were c.688g＞t (p.E230X) mutation of Pax6 gene,and 3 of 5 sporadic patients carried c.468g＞a (p.W156X),c.613c＞t (p.Q205X) and c.141 +2t＞c mutant of Pax6 gene,and the c.688g＞t (pE230X) mutation was a novel-discovered mutation.No any mutation in Pax6,Elp4 gene and SIMO fragment was detected in 1 patient from AN-02 family,2 patients from AN-03 family and 2 sporadic patients by both direct sequencing and MLPA validation.No above-mentioned mutation was found in 500 normal individuals.Conclusions The mutation of Pax6 gene is a pathogenic mutation in congenital aniridia patients,and c.688g＞t (p.E230X) is a novel Pax6 mutant,which expanded the mutation spectrum of Pax6 gene.

PKD2 mutation in an Iranian autosomal dominant polycystic kidney disease family with misleading linkage analysis data

BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic renal disorder caused by mutation in 2 genes PKD1 and PKD2. Thus far, no mutation is identified in approximately 10% of ADPKD families, which can suggest further locus heterogeneity. Owing to the complexity of direct mutation detection, linkage analysis can initially identify the responsible gene in appropriate affected families. Here, we evaluated an Iranian ADPKD family apparently unlinked to both PKD1 and PKD2 genes. This is one of the pioneer studies in genetic analysis of ADPKD in Iranian population. METHODS: Linkage reanalysis was performed by regenotyping of flanking microsatellite markers in 8 individuals of the ADPKD family. Direct mutation analysis was performed by Sanger sequencing. RESULTS: Mutation analysis revealed a pathogenic mutation (c.1094+1G>A) in the PKD2 gene in the proband. Analyzing 2 healthy and 4 clinically affected members confirmed the correct segregation of the mutation within the family and also ruled out the disease in 1 suspected individual. Misinterpretation of the linkage data was due to the occurrence of 1 crossing over between the PKD2 intragenic and the nearest downstream marker (D4S2929). Homozygosity of upstream markers caused the recombination indistinguishable. CONCLUSION: Although analysis of additive informative polymorphic markers can overcome the misleading haplotype data, it is limited because of the lack of other highly polymorphic microsatellite markers closer to the gene. Direct mutation screening can identify the causative mutation in the apparently unlinked pedigree; moreover, it is the only approach to achieve the confirmed diagnosis in individuals with equivocal imaging results.

Analysis of deafness-related gene mutations in 88 non-syndromic hearing loss patients in Fuzhou city / 中国耳鼻咽喉头颈外科

OBJECTIVE To investigate the deafness-related gene mutation frequency and hotspots in patients of Fuzhou city with non-syndromic hearing loss (NSHL). METHODS Peripheral blood samples were obtained from 88 cases of patients with hearing loss after clinical history inquiry and clinical examination. Their genomic DNA was extracted from peripheral blood by extraction kits to undergo polymerase chain reaction, traditional capillary electrophoresis sequencing and High-throughput sequencing so as to detect the mutations of deafness-related gene. RESULTS Among the 88 patients with NSHL, the gene mutation frequency was 34.09%.In the patients, 14 cases had mitochondrial 12 S rRNA mutations, six cases had GJB2 gene mutations and three cases had SLC26A4 mutations, two cases had MYO15A mutations, the other five cases had MYO7A, OTOF, TECTA, TMC1 and ILDR1 gene mutation respectively. CONCLUSION Among the 88 patients with NSHL, the most frequent mutation causing hereditary deadness was mutation in mitochondrial 12 S rRNA, followed by GJB2 and SLC26A4, The other genes such as MYO7A, OTOF, TECTA, TMC1 and ILDR1 gene were infrequent. The study could provide theoretical reference in genetic diagnosis, prevention and cure of hearing loss.

Analysis on effects of the neonatal hearing screening combined with deafness genes screening in Huzhou / 中国耳鼻咽喉头颈外科

OBJECTIVETo explore the clinical value of the neonatal hearing combined with deafness gene screening.METHODSFrom February 2014 to August 2015, 1933 newborns were included in the study. We analyzed the effects of combined screening of hearing and deafness gene.RESULTSAmong all the 1933 neonates, 71.34% (1379/1933) passed and 28.66% (554/1933) failed the initial hearing screening.The hearing impairment rate was 4.14‰ (8/1933). Genetic screening mutation rate was counted. GJB2 mutation rate was 28.97‰ (56/1933). SLC26A4 mutation rate was 13.97‰ (27/1933). GJB3 mutation rate was 6.21‰ (12/1933). Mitochondrial 12 S rRNA gene mutation rate was 1.03‰ (2/1933). 1 case of 235 delc homozygous mutation did not pass the initial hearing screening and lost to follow-up rescreening. 2 cases of 12 S rRNA 1555A>G homogeneous mutations passed early hearing screening. 8 cases of auditory handicaps were all normal.CONCLUSIONDeafness gene screening can make up for the deficiencies of the universal newborn hearing screening. Joint use of both of them should complement each other and play the biggest role.

New Lung Cancer Panel for High-Throughput Targeted Resequencing

We present a new next-generation sequencing-based method to identify somatic mutations of lung cancer. It is a comprehensive mutation profiling protocol to detect somatic mutations in 30 genes found frequently in lung adenocarcinoma. The total length of the target regions is 107 kb, and a capture assay was designed to cover 99% of it. This method exhibited about 97% mean coverage at 30x sequencing depth and 42% average specificity when sequencing of more than 3.25 Gb was carried out for the normal sample. We discovered 513 variations from targeted exome sequencing of lung cancer cells, which is 3.9-fold higher than in the normal sample. The variations in cancer cells included previously reported somatic mutations in the COSMIC database, such as variations in TP53, KRAS, and STK11 of sample H-23 and in EGFR of sample H-1650, especially with more than 1,000x coverage. Among the somatic mutations, up to 91% of single nucleotide polymorphisms from the two cancer samples were validated by DNA microarray-based genotyping. Our results demonstrated the feasibility of high-throughput mutation profiling with lung adenocarcinoma samples, and the profiling method can be used as a robust and effective protocol for somatic variant screening.

Mutation of Cx32 gene,clinical and electrophysiological features in patients with Charcot-Marie-Tooth disease / 临床神经病学杂志

Objective To investigate the mutation of Cx32 gene,clinical and electrophysiological features of Chinese patients with Charcot-Marie-Tooth(CMT) disease.Methods 24 CMT probands were selected for Cx32 mutation screening after the exclusion of the CMT1A 1.5 Mb duplication and male-to-male transmission.The motor and sensory nerve conduction studies were performed in all probands and most of their affected family members to establish the clinical CMT1,CMT2 or CMT intermediate diagnosis.The presence of mutations in the coding region of Cx32 was detected by single-strand conformation polymorphism analysis combined with direct sequencing.Results It was found 7 different point mutations in the coding region of Cx32 in 1 sporadic CMT1 patient and 6 X-linked inherited families,including 4 families with CMT1 diagnosis and 2 families with CMT intermediate diagnosis.There were 20 male CMTX patients,6 female CMTX patients and 12 asymptomatic female carriers among 38 family members bearing Cx32 mutation.All of the 26 patients were mildly to moderately affected clinically.Conclusions Seven different Cx32 point mutations were detected and the percentage of Chinese CMT families with Cx32 mutation is about 10% in our study.The inheritance model of CMT secondary to Cx32 mutation could be X-linked dominant,X-linked recessive or sporadic.Male patients are usually more severly affected than females with slower nerve conduction velocities.Cx32 mutation screening should be firstly performed in those CMT families without male-to-male transmission and CMT1A duplication.