Fast clinical molecular diagnosis of hyperphenylalaninemia using next-generation sequencing-based on a custom AmpliSeq™ panel and Ion Torrent PGM sequencing.

Hyperphenylalaninemia (HPA) can be classified into phenylketonuria (PKU) and tetrahydrobiopterin deficiency (BH4D), according to the defect of enzyme activity, both of which vary substantially in severity, treatment, and prognosis of the disease. To set up a fast and comprehensive assay in order to achieve early etiological diagnosis and differential diagnosis for children with HPA, we designed a custom AmpliSeq™ panel for the sequencing of coding DNA sequence (CDS), flanking introns, 5' untranslated region (UTR) and 3' UTR from five HPA-causing genes (PAH, PTS, QDPR, GCH1, and PCBD1) using the Ion Torrent Personal Genome Machine (PGM) Sequencer. A standard group of 15 samples with previously known DNA sequences and a test group of 37 HPA patients with unknown mutations were used for assay validation and application, respectively. All variations were confirmed by Sanger sequencing. In the standard group, all the known mutations were detected and were consistent with the results of previous Sanger sequencing. In the test group, we identified mutations in 71 of 74 alleles, with a mutation detection rate of 95.9%. We also found a frame shift deletion p.Ile25Metfs*13 in PAH that was previously unreported. In addition, 1 of 37 in the test group was inconsistent with either the molecular diagnosis or clinical diagnosis by traditional differential methods. In conclusion, our comprehensive assay based on a custom AmpliSeq™ panel and Ion Torrent PGM sequencing has wider coverage, higher throughput, is much faster, and more efficient when compared with the traditional molecular detection method for HPA patients, which could meet the medical need for individualized diagnosis and treatment.

[Detection of homozygous deletions in spinal muscular atrophy with genomic DNA sequencing].

OBJECTIVE: To detect homozygous deletions of survival motor neuron (SMN) gene with genomic DNA sequencing, and to assess the value of genetic testing for the diagnosis of spinal muscular atrophy (SMA). METHODS: Polymerase chain reaction (PCR) was used for amplifying SMN gene in 100 SMA patients and 110 controls. Four different bases (g.31957, g.32006, g.32154 and g.32269) between SMN1 and SMN2 within the amplified segments were identified with genomic DNA sequencing. Homozygous deletion of SMN1 or SMN2 was determined by the presence or absence of base peaks at such four sites. Multiplex ligation-dependent probe amplification (MLPA) was carried out to confirm the results of genomic DNA sequencing. RESULTS: In the 100 SMA samples, only SMN2 specific base peaks were detected at the four sites, for which the copy numbers of SMN1 and SMN2 was 0:2 or 0:3, suggesting homozygous deletion of SMN1 gene. By contrast, only SMN1 specific base peaks were detected in 5 samples, for which the ratio of SMN1:SMN2 was 2:0, indicating homozygous deletion of SMN2. At four different sites, SMN1/SMN2 heterozygous peaks were detected in the remaining 105 samples, for which SMN1:SMN2was 2:2, suggesting non-deletion of SMN1 or SMN2. The results of sequencing were consistent with those of MLPA. CONCLUSION: Genomic DNA sequencing is a rapid, accurate and economic method for the diagnosis of homozygous deletion of SMA.

[Limitation of PCR-RFLP method for the detection of genetic mutations in spinal muscular atrophy].

OBJECTIVE: To explore the applicability and limitation of PCR-restriction fragment length polymorphism (PCR-RFLP) method for genetic diagnosis of spinal muscular atrophy (SMA). METHODS: PCR-RFLP was applied to detect potential deletion in exons 7 and 8 of SMN1 gene in 935 suspected cases with SMA. Multiplex ligation-dependent probe amplification(MLPA) was carried out to analyze dosage alteration of SMN1 gene in 339 of such cases. To confirm the accuracy of PCR-RFLP method for homozygous and heterozygous deletions detection, the consistency of PCR-RFLP and MLPA results were assessed with a Pearson Chi-square test. RESULTS: Homozygous deletion of exon 7 of SMN1 was detected in 590 suspected cases. The rate of diagnosis was therefore 63.1% (590/935). For the 339 suspected cases, PCR-RFLP and MLPA respectively identified 194 and 196 homozygous deletions in the exon 7 of SMN1 gene, suggesting a good consistency (98.9%)(Chi-square = 0.2, P = 0.88). However, only 4 of 339 cases was found to carry a heterozygous deletion of SMN1 exon 7 by PCR-RFLP, in contrast with 17 detected by MLPA. The consistency only reached 23.5%, for which statistical significance was detected (Chi-square = 8.29, P< 0.01). CONCLUSION: Although PCR-RFLP is a simple, specific and efficient method for SMA diagnosis, it has obvious limitation for the diagnosis of 5%-10% SMA patients who have carried a compound heterozygous mutation.

[Analysis of survival motor neuron gene conversion in patients with spinal muscular atrophy].

OBJECTIVE: To investigate the type and frequency of gene conversion from SMN1 to SMN2 in Chinese patients affected with spinal muscular atrophy (SMA), and to explore the relationship between gene conversion and clinical phenotype. METHODS: Non-homozygous deletion of SMN1 gene exon 8 was screened among 417 patients with SMN1 exon 7 homozygous deletions. To analyze and verify the types of gene conversion, genomic DNA sequencing, multiplex ligation-dependent probe amplification (MLPA), and gene subcloning and sequencing were carried out. RESULTS: Thirty-one patients (7.4% of all) with non-homozygous deletions of SMN1 exon 8 were detected. Through series of experiments, the fusion genes SMN1/SMN2 in all cases were delineated. Five types of gene conversions were identified, which included SMN2-I7b/SMN1 E8, SMN2-I7a/SMN1 I7b, SMN2-E7/SMN1 I7a, SMN1 I6/SMN2 E7/SMN1 I7a and SMN2-E7/SMN1 I7a/SMN2 I7b. Such conversions were found in the type I-III patients. For 10 patients with type I-III SMA and 3 copies of SMN2 gene produced by conversion, the average survival age was 5 year and 4 months. CONCLUSION: Partial conversions of SMN1 gene have been found among Chinese SMA patients. The type of conversion and frequency seem to be different from those of other races. Gene conversion to some extent may impact on survival time and rate of SMA patients, especially type I SMA.

[Point mutation analysis of SMN1 gene in patients with spinal muscular atrophy].

OBJECTIVE: To identify the point mutations in survival motor neuron gene 1 SMN1 gene and confirm the existence of compound heterozygous mutations in Chinese patients with spinal muscular atrophy (SMA). METHODS: Three unrelated patients were diagnosed and clinically typed according to the criteria of proximal SMA established by the International SMA Consortium. Multiplex ligation-dependent probe amplification (MLPA) analysis was carried out to measure the copy numbers of SMN1, SMN2 and neuronal apoptosis inhibitory protein gene (NAIP)in the patients. The point mutation analysis of SMN1 gene was performed by reversed transcript-polymerase chain reaction (RT-PCR) and cloning sequencing. The MLPA assay and point mutation analysis were also performed in the family members to confirm the transmission of the mutations. RESULTS: Two point mutations were identified in the present study, i.e., the p.Leu228X in one patient and p.Arg288Met in two patients. The mutation p.Arg288Met was first reported in Chinese and p.Leu228X was first reported in Mainland Chinese. The case carrying p.Leu228X mutation was diagnosed as SMA I with 2 copies of SMN2, and the cases with p.Arg288Met were diagnosed as SMA I and SMA II , respectively, with 3 copies of SMN2 gene. CONCLUSION: The mutations p.Leu228X and p.Arg288Met caused severe clinical phenotypes, SMA I or SMA II. This study suggested that the compound heterozygous mutations of SMN1 existed in Chinese SMA patients, which was rarely reported previously in Chinese. It was necessary to detect the point mutation in SMN1 for genetic diagnosis of those patients with heterozygous deletion of SMN1, which would be beneficial to prenatal diagnosis and genetic counseling in these families.

[A study on genetic diagnosis for Angelman syndrome].

OBJECTIVE: To study the genetic diagnosis of Angelman syndrome(AS), and provide information for clinic diagnosis and counseling to AS families. METHODS: Methylation specific-PCR (MS-PCR) was used for primary diagnosis of 16 clinically suspected AS cases, and linkage analysis by short tandem repeat (STR) was applied to detect the molecular genetic defect in the nuclear families. RESULTS: In this study, 10 AS patients were identified by MS-PCR, and 9 of them with maternal deletion in chromosome 15q11-q13, 1 with imprinting defect in chromosome 15q11-q13 were confirmed by STR linkage analysis. CONCLUSION: Most of the AS patients could be confirmed by MS-PCR. And STR linkage analysis can detect the molecular defect of AS. It is very important for disease diagnosis, genetic counseling and prenatal diagnosis to perform the related genetic diagnosis.

[Quantitative analysis of SMN1 and SMN2 genes based on DHPLC: a reliable method for detection of non-homozygous patients with spinal muscular atrophy].

OBJECTIVE: To develop a rapid and reliable approach for testing the copy number of survival motor neuron (SMN) gene and analyze the compound heterozygous deletions of SMN1 gene. METHODS: Peripheral blood samples were collected from 38 non-homozygous deletion pediatric patients with SMA, 30 homozygous deletion patients with SMA, and 35 un-related healthy persons. SMN1 and SMN2 genes were amplified separately with allele-specific PCR (AS-PCR). Meanwhile, two irrelevant genes were amplified as internal quality control respectively. The copy numbers of SMN1 and SMN2 were determined by denaturing high-performance liquid chromatography (DHPLC). RESULTS: (1) A protocol combining multiplex allele-specific PCR and DHPLC was developed to separate SMN1 and SMN2 and to determine the copy numbers of them. The copy numbers of SMN1 and SMN2 varied from 1 to 4 and a clear-cut differentiation among the different copy number ranges could be observed for the two genes. (2) One single copy of SMN1 were detected in 20 of the 38 non-homozygous deletion patients with SMA (52.6%). Heterozygous deletions were determined in these 20 patients. Two copies of SMN2 were detected in 15 of the 20 patients with one copy of SMN1 (75.0%, 15/20). Other 5 of the 20 patients were with 3 copies of SMN2 (25.0%, 5/20). (3) One single copy of SMN1 was detected in 24 of the 30 (80%) parents of SMA patients with homozygous deletion. CONCLUSION: SMN copy number can be rapidly and reliably determined by the method of multiplex AS-PCR combined with DHPLC.

[Mutation analysis and one novel mutation detection of 6-pyruvoyl tetrahydropterin synthase gene in children with tetrahydrobiopterin deficiency].

OBJECTIVE: To investigate the distribution character of the mutations of 6-pyruvoyl tetrahydropterin synthase (PTPS) gene and to provide effective basis for gene diagnosis of tetrahydrobiopterin deficiency (BH4D) in children with hyperphenylalaninemia. METHODS: Direct sequencing was performed for screening the PTPS gene mutations in 5 patients with clinically suspected BH4D and their parents. The nature of the novel mutations were deduced by the sequences alignment and the structural analysis of mutant protein. Artificial construct restriction site was used to detect the novel mutation in the control samples. The dates of urinary pterin analysis and BH4 loading test were retrospectively analyzed after gene analysis. RESULTS: Four PTPS gene mutations (N52S, P87S, D96N, and L127F) were detected in our study. The genotypes of four PTPS deficiency patients were identified as N52S/L127F, P87S/D96N, N52S/D96N, and D96N/ -. As a novel mutation that has not been reported previously, the mutation L127F was not detected in 50 normal controls. This novel mutation L127F was inherited from the patient's mother, and this mutant site was highly conserved by sequences alignment and the protein structural analysis. Four of the five cases with hyperphenylalaninemia and suspicious BH4D, whose urinary biopterin percentage was lower than 2% , were diagnosed as PTPS deficiency during 5-20 months old. The remaining one case was excluded from BH4D. CONCLUSIONS: The mutant characterization of PTPS gene was coincident with other early studies in Chinese. The novel mutation L127F was considered as a pathogenetic mutation and associated with severe clinical phenotype.

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.

[The mutant spectrum of phenylalanine hydroxylase gene in Northern Chinese].

OBJECTIVE: To understand the mutant spectrum of phenylalanine hydroxylase (PAH) gene in Northern Chinese. METHODS: All the exons and flaking introns of PAH gene were detected by PCR-single strand conformation polymorphism (PCR/SSCP) and sequencing in 230 patients with phenylketonuria (PKU). RESULTS: (1) A total of 75 different mutations were detected in 435 out of 460 mutant alleles (94.6%). Among them 3 mutations (S251-R252>SfsX89, Y387D and A389G) have not been reported previously. The mutations, R243Q, EX6-96A>G, R111X, R413P and Y356X, were the prevalent mutations with relative frequencies of 21.7%, 10.2%, 8.3%, 6.5%, and 6.1% respectively, followed by V399V(4.1%), IVS4-1G>A (3.5%), IVS7+2T>A (2.2%) and R241C(2.2%). Most mutations were detected in exons 3, 5, 6, 7, 11 and 12 and flaking introns of PAH gene. (2) Ten polymorphism sites were detected in the study. Four sites, IVS3-22C>T, IVS10+97G>A, Q232Q and V245V, had high relative frequencies of 56.7%, 75.9%, 89.0% and 81.9% respectively. It would suggest that the race diversity exists in PAH cDNA sequence. CONCLUSION: The mutation spectrum of PAH gene in Northern Chinese is similar to other Asian populations but significantly different from European populations.

p.Val19Glyfs*21 and p.Leu228* variants in the survival of motor neuron 1 trigger nonsense-mediated mRNA decay causing the SMN1 PTC+ transcripts degradation.

Spinal Muscular Atrophy (SMA) results from loss-of-function mutations in the survival of motor neuron 1 (SMN1) gene. Our previous research showed that 40% of variants were nonsense or frameshift variants and SMN1 mRNA levels in the patients carrying these variants were significantly decreased. Here we selected one rare variant (p.Val19Glyfs*21) and one common variant (p.Leu228*) to explore the degradation mechanism of mutant transcripts. The levels of full-length (FL)-SMN1 transcripts and SMN protein in the cell lines from the patients with these variants were both significantly reduced (p<0.01). Treatment with two translation inhibitors (puromycin and Cycloheximide (CHX)) markedly increased the levels of FL-SMN1 transcripts with premature translation termination codons (PTCs) (p<0.01) and showed time-dependent (10h>5.5h) but not dose-dependent effects. Moreover, the knockdown of UPF1, a key factor in nonsense-mediated mRNA decay (NMD) by lentivirus, led to a 3.1-fold increase (p<0.01) in FL-SMN1 transcript levels in patient fibroblasts. Our research provides evidence that these two PTC-generating variants (p.Val19Glyfs*21 and p.Leu228*) can trigger NMD, causing rapid degradation of SMN1 transcripts thereby resulting in SMN protein deficiency. These two variants are highly pathogenic and are associated with more severe SMA phenotypes. Varying NMD efficiency after treatment with puromycin and CHX in different cell types was also observed.

[Detection of the prevalent mutations of 6-pyruvoyl-tetrahydropterin synthase gene by PCR-RFLP analysis in Chinese patients].

OBJECTIVE: To establish a single and rapid method for detecting the prevalent mutations of 6-pyruvoyl-tetrahydropterin synthase (PTPS) gene in Chinese patients with 6-pyruvoyl-tetrahydropterin synthase deficiency (PTPSD). METHODS: PCR-restriction fragment length polymorphism (PCR-RFLP) was used to detect three prevalent PTPS gene mutations in 4 cases of tetrahydrobiopterin deficiency (BH4D) and their parents, which was performed by the artificial construct restriction site (ACRS). PCR-RFLP included Hpa I digestion for the detection of mutation N52S (155A to G), Hae III for P87S (259C to T) and Eco R I for D96N(286G to A). The mutations of PTPS gene were confirmed by direct sequencing. RESULTS: The genotypes of 4 PTPS deficient patients were identified: N52S/-, P87S/D96N, N52S/D96N and D96N/-. The result of direct sequencing was coincident with that of PCR-RFLP analysis. CONCLUSION: (1) The PCR-RFLP analysis formed by ACRS would be a good way for detecting the three prevalent PTPS gene mutations in Chinese patients with PTPSD. (2)The PTPS gene analysis is very important for all patients with hyperphenylalaninemia, which would be useful for early clinical diagnosis and correct treatment of BH4D patients.

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-Δ7, fl/Δ7), 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.

A rare variant (c.863G>T) in exon 7 of SMN1 disrupts mRNA splicing and is responsible for spinal muscular atrophy.

Proximal spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by deletion or mutation of SMN1 (survival motor neuron 1). SMN exon 7 splicing is regulated by a number of exonic and intronic regulatory sequences and the trans-factors that bind them. Variants located in or near these regulated regions should be evaluated to determine their effect on splicing. We identified the rare variant c.863G>T (r.835_*3del, p.Gly279Glufs*5) in exon 7 of SMN1 in three patients affected with type I or type II SMA. Most of the SMN1 transcripts exhibited complete loss of exon 7 in vivo. The ex vivo splicing assay demonstrated that the variant disrupts inclusion of exon 7 (~85%) in the SMN1 mRNA; replacement with various bases yielded a variety of splicing effects in SMN1 and SMN2 pre-mRNA. The c.863G>T (r.835_*3del, p.Gly279Glufs*5) variant is located in a region that includes binding sites for multiple splicing factors including Tra2ß1. Thus, the variant disrupts Tra2ß1 binding, but does not affect binding of hnRNP A1. These findings demonstrate how rare variants influence pre-mRNA splicing of SMN and reveal the functional influence of c.863G>T (r.835_*3del, p.Gly279Glufs*5) variant in patients with SMA.

Mutation Spectrum of the Survival of Motor Neuron 1 and Functional Analysis of Variants in Chinese Spinal Muscular Atrophy.

Proximal spinal muscular atrophy (SMA) is a common fatal autosomal recessive disorder caused by deletion or mutation of the survival of motor neuron 1 (SMN1). Here, we studied SMA molecular pathology in 653 Chinese patients and found approximately 88.2% with homozygous SMN1 exon 7 deletion and 6.3% with heterozygous exon 7 loss using multiplex ligation-dependent probe amplification. SMN1 variants were detected in 34 patients with heterozygous SMN1 loss by clone sequencing. In 27 of them, 15 variants were identified: five were unreported novel variants [c.-7_9del(p.0), p.Tyr109Cys, p.Ile249Tyrfs*16, p.Tyr272Trpfs*35, and c.835-5T>G], five were previously found only in Chinese patients (p.Ser8Lysfs*23, p.Gln14*, p.Val19Glyfs*21, p.Leu228*, and p.Tyr277Cys), and five were reported in other populations [p.Ala2Gly, p.Gln15*, p.Glu134Lys, p.Ser230Leu, and c.863G>T (r.835_*3del, p.Gly279Glufs*5)]. Variants p.Ser8Lysfs*23 and p.Leu228* were the most common in Chinese SMA. Five variants (p.Ser8Lysfs*23, p.Gln14*, p.Gln15*, p.Val19Glyfs*21, and p.Leu228*) resulted in premature stop codons, likely causing SMN1 mRNA nonsense-mediated decay. The novel variant c.-7_9del (p.0) caused deletion of the translation start codon (AUG), resulting in full-length SMN protein loss. The novel variant c.835-5T>G, located in a splice site, resulted in 90% exon 7 skipping. Our study could facilitate early diagnosis for SMA patients in mutation detection and revealed the specific mutation spectrum of SMN1 in Chinese SMA and high genetic heterogeneity in subtle variants observed between patients from China and Caucasians.

Association of copy numbers of survival motor neuron gene 2 and neuronal apoptosis inhibitory protein gene with the natural history in a Chinese spinal muscular atrophy cohort.

We evaluated survival motor neuron 2 (SMN2) and neuronal apoptosis inhibitory protein (NAIP) gene copy distribution and the association of copy number with survival in 232 Chinese spinal muscular atrophy (SMA) patients. The SMN2 and NAIP copy numbers correlated positively with the median onset age (r = 0.72 and 0.377). The risk of death for patients with fewer copies of SMN2 or NAIP was much higher than for those with more copies (P < .01). The survival probabilities at 5 years were 5.1%, 90.7%, and 100% for 2, 3, and 4 SMN2 copies and 27.9%, 66.7%, and 87.2% for 0, 1, and 2 NAIP copies, respectively. Our results indicated that combined SMN1-SMN2-NAIP genotypes with fewer copies were associated with earlier onset age and poorer survival probability. Better survival status for Chinese type I SMA might due to a higher proportion of 3 SMN2 and a lower rate of zero NAIP.

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.

Subtle mutation detection of SMN1 gene in Chinese spinal muscular atrophy patients: implication of molecular diagnostic procedure for SMN1 gene mutations.

Spinal muscular atrophy (SMA) is a common autosomal recessive neuromuscular disorder caused by mutations of the survival of motor neuron 1 (SMN1) gene. Approximately 90-95% of SMA patients have a homozygous deletion of SMN1, and 5-10% of patients are believed to have subtle mutations. The molecular diagnosis of SMN1 subtle mutations is hampered by a highly homologous SMN2 gene. It is important to establish a rational molecular diagnostic procedure for SMN1 subtle mutations. We analyzed the SMN1 mutations in nine nonhomozygous patients by the following procedures: multiplex ligation-dependent probe amplification, genomic sequencing, T-A cloning on cDNA or genomic level, and/or real-time quantitative analysis. By the above molecular diagnostic procedure, six SMN1 subtle mutations, including c.5C>G(p.Ala2Gly), c.22_23 insA (p.Ser8LysfsX23), c.40G>T(p.Glu14X), c.43C>T(p.Gln15X), c.683T>A(p.Leu228X), and c.56delT(p.Val19GlyfsX21), were identified in nine Chinese patients. p.Glu14X has not been reported previously. Compared with the level of full-length SMN1 transcripts in the healthy carriers (14.1±4.5), the patient with p.Ala2Gly had no significant reduction (13.9±3.64, p=0.955). However, the levels in the patients carrying other mutations were significantly reduced (0.27±0.139 to 13.9±3.64, p=0.000-0.004). We present a reliable and rational diagnostic procedure for SMN1 subtle mutations, which would be helpful in molecular diagnosis of SMA compound heterozygotes. Our work extends the SMN1 mutation spectrum.

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

Crigler-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 UGT1A1, 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.Val386Phe), were identified. In patient B, we found that this patient had lost heterozygosity of the UGT1A1 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 UGT1A1 mutations in two CN-I patients: c.239_245delCTGTGCC (p.Pro80HisfsX6), c.1253delT (p.Met418ArgfsX5), and c.1156G>T (p.Val386Phe). The former two mutations are pathogenic; however, the pathogenic mechanism of c.1156G>T (p.Val386Phe) is unknown.