Diagnosis of Spinal Muscular Atrophy: A Simple Method for Quantifying the Relative Amount of Survival Motor Neuron Gene 1/2 Using Sanger DNA Sequencing / 中华医学杂志(英文版)

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.

Detection of homozygous deletions in spinal muscular atrophy with genomic DNA sequencing / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>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).</p><p><b>METHODS</b>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.</p><p><b>RESULTS</b>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.</p><p><b>CONCLUSION</b>Genomic DNA sequencing is a rapid, accurate and economic method for the diagnosis of homozygous deletion of SMA.</p>

Limitation of PCR-RFLP method for the detection of genetic mutations in spinal muscular atrophy / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To explore the applicability and limitation of PCR-restriction fragment length polymorphism (PCR-RFLP) method for genetic diagnosis of spinal muscular atrophy (SMA).</p><p><b>METHODS</b>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.</p><p><b>RESULTS</b>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).</p><p><b>CONCLUSION</b>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.</p>

Compound mutations (R237X and L375P) in the fumarylacetoacetate hydrolase gene causing tyrosinemia type I in a Chinese patient / 中华医学杂志(英文版)

<p><b>BACKGROUND</b>Mutations in fumarylacetoacetate hydrolase (FAH) gene can lead to tyrosinemia type 1 (HT1), a relatively rare autosomal recessive disorder. To date, no molecular genetic defects of HT1 in China have been described. We investigated a Chinese family with a HT1 child to identify mutations in FAH.</p><p><b>METHODS</b>DNA sequencing was used for mutations screening in FAH gene. Real-time polymerase chain reaction (PCR) was performed to determine the FAH gene expression level. To confirm the presence of degradation by the nonsense-mediated mRNA decay pathway (NMD), the fragments containing R237X mutations were analyzed by primer introduced restriction analysis-polymerase chain reaction (PIRA-PCR) and cDNA sequencing. Finally, the effects of the mutations reported in this study were predicted by online softwares.</p><p><b>RESULTS</b>A boy aged 3 years and 8 months was diagnosed clinically with HT1 based on his manifestations and biochemical abnormalities. Screening of FAH gene revealed two heterozygous mutations R237X and L375P transmitted from his mother and father respectively. In this pedigree, the amount of FAH mRNA relative to a healthy control was 0.44 for the patient, 0.77 for his mother and 1.07 for his father. Moreover, both PIRA-PCR and cDNA sequencing showed significant reduction of the FAH mRNA with R237X nonsense mutation. The missense mutation of L375P was not reported previously and prediction software showed that this mutation decreased the stability of protein structure and affected protein function.</p><p><b>CONCLUSIONS</b>This is the first case of HT1 analyzed by molecular genetics in China. The R237X mutation in FAH down- regulates the FAH gene expression, and the L375P mutation perhaps interrupts the secondary structure of FAH protein.</p>

Point mutation analysis of SMN1 gene in patients with spinal muscular atrophy / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>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).</p><p><b>METHODS</b>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.</p><p><b>RESULTS</b>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.</p><p><b>CONCLUSION</b>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.</p>

Analysis of survival motor neuron gene conversion in patients with spinal muscular atrophy / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>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.</p><p><b>METHODS</b>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.</p><p><b>RESULTS</b>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.</p><p><b>CONCLUSION</b>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.</p>

Compound heterozygous mutation in two unrelated cases of Chinese spinal muscular atrophy patients / 中华医学杂志(英文版)

<p><b>BACKGROUND</b>Infantile proximal spinal muscular atrophy (SMA) is a common autosomal recessive neuromuscular disorder. Approximately 90% - 95% cases of SMA result from homozygous deletion of survival motor neuron gene 1 (SMN1) and 5% cases are caused by compound heterozygous mutation (a SMN1 deletion on one allele and a subtle mutation on the other allele).</p><p><b>METHODS</b>In this research, two unrelated patients were clinically diagnosed according to the criteria of proximal SMA. Genetic diagnosis was performed to detect the homozygous deletion of exon 7 of SMN1 by PCR-restriction fragment length polymorphism (RFLP) and genomic sequencing. Multiplex ligation-dependent probe amplification (MLPA) analysis was carried out to measure copy numbers of SMN1, SMN2 and neuronal apoptosis inhibitor protein (NAIP) in the patients. Further sequencing of SMN1 allele-specific PCR (AS-PCR) and SMN1 clones were also performed to analyze the point mutation of SMN1 gene. Additionally, the pedigree analysis of these two families was carried out to identify the transmission of the mutation.</p><p><b>RESULTS</b>The inconsistent results using PCR-RFLP and genomic sequencing showed homozygous deletion of exon 7 of SMN1 and heterozygous deletion accompanied with a suspicious mutation in SMN1 gene, respectively. MLPA analysis of these two cases exhibited one SMN1 copy deletion. One identical c.863G > T (p.Arg288Met) mutation was found in two cases by sequencing the SMN1 clones, which confirmed that both cases were SMA compound heterozygotes. One case showed partial conversion to form hybrid SMN (SMN2 I7/SMN1 E8) identified by clones sequencing and another case carrying 3 SMN2 implied complete conversion from SMN1 to SMN2.</p><p><b>CONCLUSION</b>p.Arg288Met is more a disease-causing mutation than a polymorphism variation, and children with this mutation may have more severe phenotypes.</p>

Mutation analysis of SMN1 gene in patients with spinal muscular atrophy / 中华儿科杂志

<p><b>OBJECTIVE</b>Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder. About 80% - 90% of SMA patients are missing both copies of SMN1, and 5% - 10% of patients are compound heterozygotes. In the present study, we aimed to analyze survival motor neuron 1 (SMN1) gene mutation in three patients with spinal muscular atrophy and their families to explore the effect of mutation on SMN protein function and the relationship between mutation and clinical phenotype.</p><p><b>METHOD</b>According to the international criterion, all patients were diagnosed by a neurologist. Patient 1 is a 5 years old boy with SMA type II. Patient 2, female, 2.5 years old, was SMA type II. Patient 3, female, 9 years old, was SMA type III. The brother of patient 3 was SMA type II, too. The age at last examination was 14 years. Genomic DNA was extracted from peripheral blood leukocytes by using standard phenol/chloroform method and total RNA was extracted from whole blood with QIAamp RNA Blood Mini Kit. PCR/RFLP was used to detect the homozygosis deletion of the SMN1 exon 7, and multiplex ligation-dependent probe amplification (MLPA) were performed to analyze the gene dosage of SMN1 and SMN2 for each patient and his/her family members; reverse transcriptase (RT)-PCR and clone sequencing were conducted for identifying the point mutation of SMN1 in three patients. The sequencing of genomic DNA and MLPA were carried out in the 3 families members to confirm the transition of mutation.</p><p><b>RESULT</b>No homozygous deletion of the SMN1 exon 7 was observed in any member of the 3 families. Case 1 and case 2 had one SMN1 copy compound with c.400G > A (p.Glu134Lys) mutation on it and SMN2 was two copies, respectively. Case 3 and her brother also had one copy of SMN1 and two copies of SMN2, and a mutation c.689C > T (p.Ser230Leu) occurred on the retained SMN1. All point mutations were from their fathers and deletion come from their mothers for SMN1 gene.</p><p><b>CONCLUSION</b>In this work, p.Glu134Lys and p.Ser230Leu mutations were identified in three unrelated families and p.Glu134Lys from two patients was first discovered in Chinese SMA. The p.Glu134Lys mutation within the SMN Tudor domain prevents the binding of SMN and Sm. The fact that p.Ser230Leu results in a polar amino acid substituted for non-polar amino acid possibly affects the structure of SMN and then damages its function. SMN1 point mutation analysis is not only advantageous to the diagnosis of those patients with heterozygous deletion of SMN1, but will be beneficial to the prenatal diagnosis and genetic counseling for their families.</p>

A novel missense mutation of the ubiquitin protein ligase E3A gene in a patient with Angelman syndrome / 中华医学杂志(英文版)

<p><b>BACKGROUND</b>Angelman syndrome (AS) is a neurogenetic disorder caused by an expression defect of the maternally inherited copy of ubiquitin protein ligase E3A (UBE3A) gene from chromosome 15. Although the most common genetic defects include maternal deletions of chromosome 15q11-13, paternal uniparental disomy and imprinting defect, mutations in the UBE3A gene have been identified in approximately 10% of AS patients.</p><p><b>METHODS</b>A Chinese girl of 28 months presented clinical manifestation of AS. Genetic diagnosis and molecular genetic defects were studied by methylation-specific PCR (MS-PCR) and linkage analysis by short tandem repeat (STR). We further performed sequence analysis of all the coding exons and flanking sequences of the UBE3A gene. The novel mutation screening was also performed in 100 unrelated healthy individuals to exclude the possibility of identifying a polymorphism variation.</p><p><b>RESULTS</b>The MS-PCR analysis of the patient showed biparental inheritance of chromosome 15 with a normal methylation pattern in the 15q11-q13 region. And STR analysis revealed that the patient also inherited biparental alleles for six microsatellites. A novel mutation, cDNA1199 C> A (p.P400H), in exon 9 of the maternal UBE3A gene, was identified in the patient. Meanwhile, the mutation was observed in the patient's mother who had a normal phenotype.</p><p><b>CONCLUSIONS</b>It is necessary to perform the UBE3A gene mutation analysis in non-deletion/non-UPD/non-ID patients with AS. The clinical picture of the patient is concordant with that observed in previously reported AS patients with UBE3A mutation.</p>

Genetic and clinical study on 17 cases of Angelman syndrome with deletion of 15q11-13 / 中华儿科杂志

<p><b>OBJECTIVE</b>Angelman syndrome (AS) is a neurodevelopmental genetic disorder that maps to 15q11-13. The primary phenotypes are attributable to loss of expression of imprinted UBE3A gene within this region which can arise by means of a number of mechanisms. The purpose of this study was to make a genetic diagnosis and to analyze the clinical features in suspected patients with AS.</p><p><b>METHOD</b>A total of 17 cases were diagnosed clinically as AS including 7 males and 10 females. The age at the time of diagnosis ranged from 8 months to 5 years. Genetic diagnosis was made by methylation-specific PCR (MS-PCR), linkage analysis by short tandem repeat (STR) and chromosome karyotype analysis. According to the international diagnostic criteria of AS, the related characteristic clinical features of the AS patients with deletion of 15q11-13 were analyzed and summarized.</p><p><b>RESULT</b>Deletion of 15q11-13 was confirmed by genetic diagnosis in 17 AS patients. No abnormal findings were observed when they were born. Developmental delay in movement, speech impairments and happy disposition were observed in 100% (17/17) AS patients. And the severe speech deficit was much easier and more obvious to observe than movement. About 80% (14/17) - 90% (15/17) AS patients presented frequent clinical characteristics, such as seizures and abnormal EEG. However, microcephaly could only be observed in 35% (6/17) AS patients. Regarding the associated findings of AS, 41% (7/17) - 77% (13/17) AS patients could be observed with flat occiput/occipital groove, prognathia, wide mouth, wide-spaced teeth, frequent drooling, excessive mouth behaviors, hypopigmented skin, light hair compared to parents, flexed arm position during ambulation and sleep disorder etc. These features occurred at a higher frequency in those patients of > 2 years old group than that of < 2 years old group.</p><p><b>CONCLUSION</b>The testing strategies of MS-PCR and STR linkage analysis combined with chromosome karyotype analysis were appropriate to the molecular genetic diagnosis of AS. In our analysis of clinical features, there was a lower rate of small head circumference (HC) in 35% patients compared with 80% patients in Caucasian with microcephaly, which might be attributable to the phenotypic heterogeneity in different races. And the birth history, movement and speech development and main clinical features of the Chinese AS patients were consistent with those of other studies. Clinical analysis in patients of different age groups showed that findings associated with AS would be more easily observed with the age increasing. Genetic diagnosis should be performed in clinically suspected AS patients.</p>

Unbalanced translocation t (5;15) in a patient with Prader-Willi syndrome / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To diagnose and detect the molecular defect in a suspected patient with Prader-Willi syndrome.</p><p><b>METHODS</b>Genetic diagnosis and molecular genetic analysis were performed by using chromosome karyotype analysis, methylation-specific PCR (MS-PCR), and linkage analysis using short tandem repeat (STR).</p><p><b>RESULTS</b>The karyotype of the patient was 45, XX, der(5), t(5;15)(q35;q13), -15, and the parents were 46, XY and 46, XX, respectively, implying that the unbalanced translocation t(5;15) in the patient was de novo. Furthermore, MS-PCR and STR linkage analysis confirmed that the patient's 15q11-13 deletion was resulted from unbalanced translocation on paternal chromosome 15.</p><p><b>CONCLUSION</b>Genetic analysis should be applied in suspected patients with Prader-Willi syndrome to confirm the diagnosis. Cytogenetic and molecular techniques would be helpful in clinical diagnosis, genetic counseling and prenatal diagnosis.</p>

A study on genetic diagnosis for Angelman syndrome / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To study the genetic diagnosis of Angelman syndrome(AS), and provide information for clinic diagnosis and counseling to AS families.</p><p><b>METHODS</b>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.</p><p><b>RESULTS</b>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.</p><p><b>CONCLUSION</b>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.</p>