Diagnosis of Spinal Muscular Atrophy:A Simple Method for Quantifying the Relative Amount of Survival Motor Neuron Gene 1/2 Using Sanger DNA Sequencing

Background: Spinal muscular atrophy (SMA) is caused by homozygous deletion or compound heterozygous mutation of survival motor neuron gene 1 (SMN1), which is the key to diagnose SMA. The study was to establish and evaluate a new diagnostic method for SMA. Methods: A total of 1494 children suspected with SMA were enrolled in this study. Traditional strategy, including multiplexed ligation-dependent probe amplification (MLPA) and TA cloning, was used in 1364 suspected SMA children from 2003 to 2014, and the 130 suspected SMA children were tested by a new strategy from 2015 to 2016, who were also verified by MLPA combined with TA cloning. The SMN1 and SMN2 were simultaneously amplified by polymerase chain reaction using the same primers. Mutation Surveyor software was used to detect and quantify the SMN1 variants by calculating allelic proportions in Sanger sequencing. Finally, turnaround time and cost of these two strategies were compared. Results: Among 1364 suspected SMA children, 576 children had SMN1 homozygous deletion and 27 children had SMN1 compound heterozygous mutation. Among the 130 cases, 59 had SMN1 homozygous deletion and 8 had heterozygous deletion: the SMN1-specific peak proportion on exon 7 was 34.6 ± 1.0% and 25.5 ± 0.5%, representing SMN1:SMN2 to be 1:2 and 1:3, respectively. Moreover, five variations, including p.Ser8Lysfs *23 (in two cases), p.Leu228*, p.Pro218Hisfs *26, p.Ser143Phefs*5, and p.Tyr276His, were detected in 6/8 cases with heterozygous deletion, the mutant allele proportion was 31.9%, 23.9%, 37.6%, 32.8%, 24.5%, and 23.6%, which was similar to that of the SMN1-specific site on exon 7, suggesting that those subtle mutations were located in SMN1. All these results were consistent with MLPA and TA cloning. The turnaround times of two strategies were 7.5 h and 266.5 h, respectively. Cost of a new strategy was only 28.5% of the traditional strategy. Conclusion: Sanger sequencing combined with Mutation Surveyor analysis has potential application in SMA diagnosis.

Association between SMN2 methylation and disease severity in Chinese children with spinal muscular atrophy

The homozygous loss of the survival motor neuron 1 （SMN1） gene is the primary cause of spinal muscular atrophy （SMA）, a neuromuscular degenerative disease. A genetically similar gene, SMN2, which is not functionally equivalent in all SMA patients, modifies the clinical SMA phenotypes. We analyzed the methylation levels of 4 CpG islands （CGIs） in SMN2 in 35 Chinese children with SMA by MassARRAY. We found that three CpG units located in CGI 1 （nucleotides （nt） -871, -735） and CGI 4 （nt ＋999） are significantly hypomethylated in SMA type III compared with type I or II children after receiving Bonferroni correction. In addition to the differentially methylated CpG unit of nt -871, the methylation level of the nt -290/-288/-285 unit was negatively correlated with the expression of SMN2 full-length transcripts （SMN2-fl）. In addition, the methylation level at nt ＋938 was inversely proportional to the ratio of SMN2-fl and lacking exon 7 transcripts （SMN2-A7, fl/A7）, and was not associated with the SMN2 transcript levels. Thus, we can conclude that SMN2 methylation may regulate the SMA disease phenotype by modulating its transcription.

Two unrelated patients with rare Crigler-Najjar syndrome type I:two novel mutations and a patient with loss of heterozygosity of UGT1A1 gene

Cdgler-Najjar syndrome type Ⅰ （CN-I） is the most severe type of hereditary unconjugated hyperbilirubinemia. It is caused by homozygous or compound heterozygous mutations of the UDP-glycuronosyltransferase gene （UGT1A1） on chromosome 2q37. Two patients clinically diagnosed with CN-I were examined in this paper. We sequenced five exons and their flanking sequences, specifically the promoter region of UGT1A 1, of the two patients and their parents. Quantitative real-time polymerase chain reaction （qRT-PCR） was used to determine the UGT1A1 gene copy number of one patient. In patient A, two mutations, c.239_245delCTGTGCC （p.Pro80HisfsX6; had not been reported previously） and c.1156G〉T （p.Va1386Phe）, were identified. In patient B, we found that this patient had lost heterozygosity of the UGTIA1 gene by inheriting a deletion of one allele, and had a novel mutation c.1253delT （p.Met418ArgfsX5） in the other allele. In summary, we detected three UGTIA 1 mutations in two CN-I patients： c.239_ 245delCTGTGCC （p.Pro80HisfsX6）, c.1253delT （p.MeH18ArgfsX5）, and c.1156G〉T （p.Va1386Phe）. The former two mutations are pathogenic; however, the pathogenic mechanism of c.1156G〉T （p.Va1386Phe） is unknown.

A novel large deletion mutation of FERMT1 gene in a Chinese patient with Kindler syndrome

Kindler syndrome （KS; OMIM 173650） is a rare autosomal recessive skin disorder, which results in symptoms including blistering, epidermal atrophy, increased risk of cancer, and poor wound healing. The majority of mutations of the disease-determining gene （FERMT1 gene） are single nucleotide substitutions, including missense mutations, nonsense mutations, etc. Large deletion mutations are seldom reported. To determine the mutation in the FERMT1 gene associated with a 7-year-old Chinese patient who presented clinical manifestation of KS, we performed direct sequencing of all the exons of FERMT1 gene. For the exons 2-6 without amplicons, we analyzed the copy numbers using quantitative real-time polymerase chain reaction （qRT-PCR） with specific primers. The deletion breakpoints were sublocalized and the range of deletion was confirmed by PCR and direct sequencing. In this study, we identified a new 17-kb deletion mutation spanning the introns 1-6 of FERMT1 gene in a Chinese patient with severe KS phenotypes. Her parents were carriers of the same mutation. Our study reported a newly identified large deletion mutation of FERMT1 gene involved in KS, which further enriched the mutation spectrum of the FERMT1 gene.

osaicism of Tetrasomy 18p： Clinical and Cytogenetic Findings in a Female Child

INTRODUCTION The tetrasomy 18p （OMIM 614290） is a very rare chromosomal abnormality, with a prevalence of 1/140,000-180,000 live births,Although it has been known in some countries, it has been seldom reported in China. Especially, mosaicism for tetrasomy 18p is even rare. Because of a very limited number of cases, the phenotypic spectrum of mosaic tetrasomy 18p, the complications, and prognosis are unknown. In this study, we reported a patient with mosaic tetrasomy 18p by conventional karyotyping analysis, high-resolution single nucleotide polymorphism （SNP） array, and fluorescence in situ hybridization （FISH）.