Identification of LINS1 gene variant in a patient with severe mental retardation / 中华医学遗传学杂志

Objective@#To explore the genetic basis of a child with idiopathic mental retardation.@*Methods@#Clinical data and peripheral blood sample of the child were collected. Genomic DNA was extracted and subjected to copy number analysis using single nucleotide polymrophism array comparative genome hybridization (SNP-aCGH) and targeted capture and next generation sequencing (NGS).@*Results@#No microdeletion/microduplication were detected by SNP-aCGH. NGS has detected homozygous c. 722delA(p.Asp241fs) variant of the LISN1 gene, which is known to underlie autosomal recessive mental retardation - 27 (MRT 27). Both parents are carriers of the variant, conforming to the autosomal recessive inheritance.@*Conclusion@#A novel pathogenic variant of the LINS1 gene has been identified, which probably underlies the MRT 27 in the patient.

Rapid identification of pathogenic mutations in sporadic hereditary retinal dystrophies using targeted next-generation sequencing / 中华实验眼科杂志

Background Hereditary retinal diseases (HRDs) are a group of retinal degenerative diseases with significant genetic and clinical heterogeneities.Traditional techniques are challenging for detection of pathogenic mutations.Objective This study was to identify the diseasing-causal genes in 20 Chinese families with a variety of HRDs.Methods Family histories and ophthalmic examinations were obtained from all participants in 20 sporadic families.Targeted sequence capture array technique with next-generation sequencing (NGS) was performed to detect pathogenic mutations in 232 identified genes associated with HRDs.Variants detected by NGS were filtered by bioinformatic analysis HRDs.Genotype-phenotype correlation was also assessed.Results We identified 11 patients with pathogenic mutations,including 8 compound heterozygous mutations and 3 homozygous mutations,which were not yet reported.These findings showed genetic diagnoses in 11 of 20 patients,with the positive rate of 55％.Among them,6 patients were autosomal recessive inheritance and 5 were unspecific.Identification of different mutations and divergent phenotypes revealed 5 patients were affected with cone-rod dystrophy,3 patients with Leber congenital amaurosis,1 patient with congenital stationary night blindness,1 patient with Best vitelliform macular dystrophy and 1 patient with Stargardt disease.Conclusions Targeted NGS is an effective approach for the genetic diagnoses of HRDs.These findings provide insights into understanding the genotype-phenotype correlations in HRDs.

Application of gene capture technology combined with next generation sequencing technology on methylmalonic acidemia / 中华实用儿科临床杂志

Objective To assess the efficiency and reliability of clinical genetic diagnosis of methylmalonic acidemia(MMA) using new generation sequencing platform (HiSeq2000).Methods 1.Nine patients diagnosed with clinical signs of MMA were recruited.DNA library from the patients were mixed with designed gene capture probe.The whole exons region of 48 genes related to organic acid metabolism were screened using the gene capture combined with high-throughput sequencing.2.The joints were removed and the low quality data were filtered,the data were analyzed by means of SNP and InDel.To avoid the false positive,the abnormal sites were verified using the Sanger sequencing method.3.The detection of the organic acid in the urine was performed through gas chromatography-mass spectrometry and other auxiliary examinations.Results 1.Gene mutation:7 gene mutations of MMACHC were identified in 7 patients.Seven mutations:c.482G ＞ A,c.567_568insT,c.609G ＞ A,c.440_441del,c.80A ＞ G,c.315C ＞ G,c.90G ＞ Awere screened.The mutation c.440_441del had not been reported before,and others were all related to the disease.Two gene mutations of mutase apoenzyme(MUT) were identified in 1 case,all of which were introns:.c.754-1G ＞ C,c.1677-1G ＞ A.The novel mutation was c.754-1G ＞ C.No gene mutation was identified in 1 patient.2.Clinical manifestation:all of the patients were development delay,but the degrees were different;3 patients with convulsion; 1 patient with headache and central facial paralysis;1 patient with repeated intractable metabolic acidosis;1 patient with repeated hemolysis.Electroencephalogram of the all patients were abnormal;the result of cranial MRI of the 8 patients were abnormal;In all patients,urine level of methylmalonic acid significantly increased (273.4-146 022.8 times).Blood homo cysteine of 8 patients were significantly increased(27.13-396.84 μmol/L,normal ＜ 20 μmol/L).3.Sanger sequencing:there were no false positive exists.Conclusions 1.There were not a correlation between the clinical manifestation and gene mutation of the patients with MMA.The c.609G ＞ A was the hotspot mutation of MMACHC gene in Chinese patients with MMA and homocysteinemia.2.The mutations c.440_441del and c.754-1G ＞ C were presumed to be novel mutations.3.Gene capture technology combined with next-generation sequencing technology could be used to interrogate the wealth of data available in the human genome and lay the foundations for counseling of gene.This platform can be readily and timely adopted by clinical molecular diagnosis of MMA and represents a high throughput,high sensitivity,high efficiency and other characteristics approach for screening common genetic diseases.

Application of Next Generation Sequencing Upon the Molecular Genetic Diagnosis of Deafness

The main objective of this review is to describe the new sequencing technologies called next generation sequencing (NGS) and its utility as a molecular genetic diagnosis tool in a medical field. Sanger method has dominated the genome sequencing industry for the past 30 years since its invention in 1975. It produced first human genome and still remains the gold standard for genome sequencing. However, it cannot meet the needs for enormous genetic data gathering and process because of its relatively long sequencing time and high cost per sample. NGS which parallelise the sequencing process, thereby increasing processing speed at a reduced cost per sample emerged to compensate for the weakness of the previous method. Currently NGS is used in some medical areas and its use is being widened. NGS also plays an important role in a study of genetically heterogenous hearing diseases. NGS is expected to mark a significant milestone in genomic research filed in a near future.