Analysis of a patient with severe Hemophilia A due to a large duplication of F8 gene / 中华医学遗传学杂志

OBJECTIVE@#To report on a case with severe hemophilia A (HA) due to a large duplication of F8 gene.@*METHODS@#Inversion detection, Sanger sequencing, and multiplex ligation-dependent probe amplification (MLPA) were used to detect the mutation in the proband and his mother.@*RESULTS@#The patient, a 7-year-old boy, was diagnosed with severe HA at 8 months. No inhibitor was developed over 150 exposure days. Intronic inversion detection and Sanger sequencing have failed to identify pathogenic variants, while MLPA revealed a large duplication [Ex 1_22 dup (2 copies)] in the proband, for which his mother was a carrier [Ex 1_22 dup (3 copies)]. Large duplications of the F8 gene have so far been found in 24 HA patients, all of whom had a severe phenotype, only one had a history of inhibitors.@*CONCLUSION@#Large duplications of F8 gene are associated with severe HA. The diagnostic rate for HA may be increased by MLPA.

Clinical phenotype and genetic analysis of MECP2 duplication syndrome / 中华医学遗传学杂志

OBJECTIVE@#To analyze the clinical symptom and parental origin of patients with MECP2 duplication syndrome in order to provide a basis for genetic counseling and prenatal diagnosis.@*METHODS@#Clinical symptoms of four patients who were diagnosed with MECP2 duplication syndrome by copy number variation sequencing (CNV-Seq) were reviewed. The maternal origin of the duplications were verified.@*RESULTS@#All patients were males, and CNV-Seq revealed that they have all harbored a duplication in the Xq28 region spanning 0.32 ~ 0.86 Mb, which were derived from asymptomatic mothers. The clinical symptoms of three patients with three copies included delayed speech, intellectual disability, and muscular hypotonia, while the patient with four copies had died at 6 months after birth, with clinical symptoms including recurrent infections, seizures, and spasticity.@*CONCLUSION@#The four cases of MECP2 duplication syndrome have shown complete penetrance and have all derived from asymptomatic mothers. As a stable and reliable method, CNV-Seq can accurately detect the MECP2 duplication syndrome.

Síndrome de Rett: Análisis molecular del gen MECP2 en pacientes chilenas / Rett syndrome: MECP2 gene molecular analysis in Chilean patients

INTRODUCCIÓN: El síndrome de Rett (RTT) es un trastorno neurológico progresivo caracterizado por producir una regresión del desarrollo psicomotor en niñas previamente sanas. La mayoría de los casos son causados por variantes patogénicas en el gen MECP2, que codifica para la proteína methyl CpG- binding protein 2. OBJETIVO: Describir la frecuencia y el tipo de variantes patogénicas en MECP2 en mujeres chilenas con diagnóstico clínico de RTT. PACIENTES Y MÉTODO: Se invitó a participar en este estudio a mujeres chilenas con sospecha clínica de RTT. Se reunió información clínica mediante un cuestionario. Se analizaron variantes patogénicas en MECP2 mediante el método de secuenciación de Sanger y se utilizó Multiple Ligation-dependant Probe Amplification (MLPA) para la detección de duplicaciones y deleciones. RESULTADO: El estudio incluyó 14 pacientes con sospecha de RTT, de las cuales 8 (57%) pacientes tuvieron variantes patogénicas. Las restantes permanecen sin diagnóstico molecular. CONCLUSIÓN: Variantes patogénicas en MECP2 están presentes en pacientes chilenas con RTT. Es probable que haya otros genes o diagnósticos involucrados en las pacientes sin hallazgos en MECP2. A partir de este trabajo, el diagnóstico molecular está disponible en Chile.

INTRODUCTION: Rett syndrome (RTT) is a progressive neurological disorder characterized by regres sion of psychomotor development in previously healthy girls. Most cases are due to pathogenic va riants in the MECP2 gene which encodes for the methyl CpG-binding protein 2. OBJECTIVE: To des cribe the frequency and type of pathogenic variants in the MECP2 gene in Chilean female patients with clinical diagnosis of RTT. PATIENTS AND METHOD: Chilean women with clinical suspicion of RTT were invited to participate in the study. Clinical data were collected through a questionnaire. MECP2 pathogenic variants were analyzed by Sanger sequencing method and Multiplex Ligation-dependent Probe Amplification (MLPA) was used to detect duplications or deletions. RESULTS: The study in cluded 14 patients with suspected RTT, of which eight (57%) patients had pathogenic variants. The other patients remain without molecular diagnosis. CONCLUSIONS: Pathogenic variants in MECP2 are present in Chilean patients with RTT. It is likely that there are other genes or diagnoses involved in patients without MECP2 findings. As of this study, molecular diagnosis is available in Chile.

Comprehensive genetic diagnosis of patients with Duchenne/Becker muscular dystrophy (DMD/BMD) and pathogenicity analysis of splice site variants in the DMD gene / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are caused by mutations in the DMD gene. The aim of this study is to identify pathogenic DMD variants in probands and reduce the risk of recurrence of the disease in affected families. Variations in 100 unrelated DMD/BMD patients were detected by multiplex ligation-dependent probe amplification (MLPA) and next-generation sequencing (NGS). Pathogenic variants in DMD were successfully identified in all cases, and 11 of them were novel. The most common mutations were intragenic deletions (69%), with two hotspots located in the 5' end (exons 2-19) and the central of the DMD gene (exons 45-55), while point mutations were observed in 22% patients. Further, c.1149+1G>A and c.1150-2A>G were confirmed by hybrid minigene splicing assay (HMSA). This two splice site mutations would lead to two aberrant DMD isoforms which give rise to severely truncated protein. Therefore, the clinical use of MLPA, NGS, and HMSA is an effective strategy to identify variants. Importantly, eight embryos were terminated pregnancies according to prenatal diagnosis and a healthy boy was successfully delivered by preimplantation genetic diagnosis (PGD). Early and accurate genetic diagnosis is essential for prenatal diagnosis/PGD to reduce the risk of recurrence of DMD in affected families.

Análisis de variación del número de copias y de patrones de metilación en la región 15q11-q13 / Variation analysis of the number of copies and methylene patterns in region 15q11-q13

La región q11-q13 del cromosoma 15 humano es proclive a sufrir alteraciones genéticas. Algunos genes de la región presentan expresión parental diferencial monoalélica, regulada por imprinting (EI). Errores en la regulación del EI, disomías uniparentales (DSU), así como también el cambio en el número de copias genómicas (CNV) producidos por sitios susceptibles de quiebre cromosómico (BP), producen alteraciones en esta región. Las enfermedades más frecuentes asociadas son el síndrome de Prader-Willi, el síndrome de Angelman y el síndrome de microduplicación 15q11-q13. En el presente trabajo analizamos la región 15q11-q13 por Methyl specific-multiplex ligation-dependent probe amplification (MS-MLPA) en 181 muestras de ADN derivadas a nuestro servicio de análisis genético molecular. En este trabajo mostramos que, de las 181 muestras, 39 presentaron alteraciones detectables por MS-MLPA. El 61.5% (24/39) de esas alteraciones detectadas fueron deleciones, el 5.1% (2/39) duplicaciones y el 33.3%(13/39) DSU/EI. Los CNV fueron 4 veces más frecuentes que las DSU/EI (OR = 4; IC 95%: 1.56-10.25) consistente con la literatura. Entre los CNV, dos casos atípicos permiten postular posibles sitios BP que no han sido informados en la literatura previamente.

Human chromosome 15q11-q13 region is prone to suffer genetic alterations. Some genes of this region have a differential monoallelic imprinting-regulated expression pattern. Defects in imprinting regulation (IE), uniparental disomy (UPD) or copy number variation (CNV) due to chromosomal breakpoints (BP) in 15q11-q13 region, are associated with several diseases. The most frequent are Prader-Willi syndrome, Angelman syndrome and 15q11-q13 microduplication syndrome. In this work, we analyzed DNA samples from 181 patients with phenotypes which were compatible with the above-mentioned diseases, using Methyl specific-multiplex ligation-dependent probe amplification (MS-MLPA). We show that, of the 181 samples, 39 presented alterations detectable by MS-MLPA. Of those alterations, 61.5% (24/39) were deletions, 5.1% (2/39) duplications and 33.3% (13/39) UPD/IE. The CNV cases were 4 times more frequent than UPD/IE (OR= 4; IC 95%: 1.56-10.25), consistent with the literature. Among the CNVs, two atypical cases allow to postulate new possible BP sites that have not been reported previously in the literature.

Genetic analysis of a 46,XY female with sex reversal due to duplication of NR0B1 gene / 中华医学遗传学杂志

OBJECTIVE@#To explore the pathogenesis of a 46,XY female with sex reversal.@*METHODS@#Peripheral blood lymphocytes of the patient were subjected to G-banding karyotype analysis. Sex chromosomes were analyzed with fluorescence in situ hybridization (FISH). SRY gene was analyzed by Sanger sequencing. The whole exome of the patient was subjected to next generation sequencing. Copy number variations (CNVs) of the NR0B1, SF1, SRY, SOX9 and WNT4 genes were validated by multiplex ligation-dependent probe amplification (MLPA).@*RESULTS@#The patient had a 46,XY karyotype. FISH analysis showed that her sex chromosomes were X and Y. No mutation was found in the SRY gene, and no pathogenic mutation was detected in her exome. However, a duplication spanning approximately 67.31 kb encompassing the MAGEB1, MAGEB3, MAGEB4 and NR0B1 genes at Xp21, was predicted by software analysis. MLPA confirmed duplication of the NR0B1 gene in the patient and her mother.@*CONCLUSION@#A duplication fragment of Xp21 encompassing the NR0B1 gene in the 46,XY female with sex reversal is transmitted from her asymptomatic carrier mother. Attention should be paid towards the insidious nature and high morbidity of this duplication.

Analysis of SCN1A deletions or duplications in patients with Dravet syndrome / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To determine the type and frequency of SCN1A deletions and duplications among patients with Dravet syndrome (DS).</p><p><b>METHODS</b>For DS patients in which no mutations of the SCN1A gene were detected by PCR-DNA sequencing, SCN1A deletions and duplications were detected by multiplex ligation-dependent probe amplification (MLPA).</p><p><b>RESULTS</b>In 680 DS patients, 489 had SCN1A mutations identified by PCR-DNA sequencing. In 191 patients who were negative for the SCN1A PCR-DNA sequencing, 15 (15/191, 7.9%) were detected with heterozygous SCN1A deletions or duplications, which included 14 (14/15, 93.3%) SCN1A deletions and 1 SCN1A duplication. There were 13 types of mutations, including whole SCN1A deletions in 3 patients, partial SCN1A deletions in 11 patients and partial SCN1A duplications in one patient. By testing the parents, 14 mutations were found to be de novo. For the remaining case, no SCN1A deletion or duplication was found in the mother, while the father was not available.</p><p><b>CONCLUSION</b>Approximately 8% of Chinese patients who were negative for SCN1A mutation by PCR-sequencing have SCN1A deletions or duplications. The MLPA analysis should be considered as an important strategy for such patients. SCN1A deletions are more common than SCN1A duplications among DS patients, and the most common types are whole SCN1A deletions. The majority of SCN1A deletions or duplications are de novo.</p>

Evolutionary and Comparative Genomics to Drive Rational Drug Design, with Particular Focus on Neuropeptide Seven-Transmembrane Receptors

Seven transmembrane receptors (7TMRs), also known as G protein-coupled receptors, are popular targets of drug development, particularly 7TMR systems that are activated by peptide ligands. Although many pharmaceutical drugs have been discovered via conventional bulk analysis techniques the increasing availability of structural and evolutionary data are facilitating change to rational, targeted drug design. This article discusses the appeal of neuropeptide-7TMR systems as drug targets and provides an overview of concepts in the evolution of vertebrate genomes and gene families. Subsequently, methods that use evolutionary concepts and comparative analysis techniques to aid in gene discovery, gene function identification, and novel drug design are provided along with case study examples.

Isolated 9p Duplication With der(Y)t(Y;9)(q12;p13.2) in a Male Patient With Cardiac Defect and Mental Retardation Confirmed by Chromosomal Microarray

No abstract available.

An 18.3-Mb Duplication on Chromosome 14q With Multiple Cardiac Anomalies and Clubfoot Was Identified by Microarray Analysis

No abstract available.

Analysis of heterozygous duplication of PMP22 gene in a pedigree affected with Charcot Marie Tooth disease / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To analyze mutation of the PMP22 gene in a pedigree affected with Charcot-Marie-Tooth disease.</p><p><b>METHODS</b>Genomic DNA was extracted from peripheral blood samples of the proband and members from his family, and fetal DNA was extracted from amniotic fluid sample. Multiplex ligation-dependent probe amplification (MLPA) and array-based comparative genomic hybridization (array-CGH) analyses were carried out to determine the copy number of the PMP22 gene. Sanger sequencing was carried out to detect point mutations of the PMP22 gene.</p><p><b>RESULTS</b>A heterozygous duplication of the PMP22 gene was detected in the proband and his father, while no point mutation, insertion or deletion was found in them. No duplication or deletion of the PMP22 gene was found in other family members.</p><p><b>CONCLUSION</b>Based on clinical symptoms and genetic findings, the heterozygous duplication of the PMP22 gene is probably the cause of the disease in the proband. The fact that the father has carried the same duplication but with no detectable symptom may be due to irregular transmission pattern of the mutation. Genetic counseling for the family should therefore be with caution.</p>

Mutation analysis of 81 cases with Duchenne/Becker muscular dystrophy / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To perform mutation analysis for 81 unrelated patients with Duchenne/Becker muscular dystrophy (DMD/BMD) from Henan Province.</p><p><b>METHODS</b>Multiplex ligation-dependent probe amplification (MLPA) was used to detect potential deletion/duplications of the DMD gene. Those with single exon deletions were validated with PCR amplification and Sanger sequencing to rule out false positive results. Patients with negative MLPA results were further analyzed with next-generation sequencing (NGS), and the result was validated by Sanger sequencing.</p><p><b>RESULTS</b>DMD gene deletion/duplications were detected in 67 cases by MLPA, and exons 45-54 was the most frequently deleted. The phenotypes of 79.1% patients with a deletion or duplication has conformed to the reading frame rule. In addition, 13 mutations were detected by NGS and Sanger sequencing, which included 6 novel mutations including one frameshift mutation c.4708-4709insTG and 5 nonsense mutations (c.8812G>T, c.2131A>T, c.6035T>A, c.3426C>A, and c.3055C>T).</p><p><b>CONCLUSION</b>This results have enriched the DMD gene mutation database. Combined MLPA, NGS and Sanger sequencing can greatly enhance the sensibility and specificity of genetic testing for the DMD/BMD.</p>

Detection of a fetus with paternally derived 2q37.3 microdeletion and 20p13p12.2 microduplication using whole genome microarray technology / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To perform prenatal diagnosis for a fetus with multiple malformations.</p><p><b>METHODS</b>The fetus was subjected to routine karyotyping and whole genome microarray analysis. The parents were subjected to high-resolution chromosome analysis.</p><p><b>RESULTS</b>Fetal ultrasound at 28+4 weeks has indicated intrauterine growth restriction, left kidney agenesis, right kidney dysplasia, ventricular septal defect, and polyhydramnios. Chromosomal analysis showed that the fetus has a karyotype of 46,XY,der(2),der(20), t(2;20)(q37.3;p12.2), t(5;15) (q12.2;q25) pat. SNP array analysis confirmed that the fetus has a 5.283 Mb deletion at 2q37.3 and a 11.641 Mb duplication at 20p13p12.2. High-resolution chromosome analysis suggested that the father has a karyotype of 46,XY,t(2;20)(q37.3;p12.2),t(5;15)(q12.2;q25), while the mother has a normal karyotype.</p><p><b>CONCLUSION</b>The abnormal phenotype of the fetus may be attributed to a 2q37.3 microdeletion and a 20p13p12.2 microduplication. The father has carried a complex translocation involving four chromosomes. To increase the chance for successful pregnancy, genetic diagnosis and/or assisted reproductive technology are warranted.</p>

Minor BCR-ABL1-Positive Acute Myeloid Leukemia Associated With the NPM1 Mutation and FLT3 Internal Tandem Duplication

No abstract available.

Characterization of the acetohydroxyacid synthase multigene family in the tetraploide plant Chenopodium quinoa

Background Currently, the technology called Clearfield® is used in the development of crops resistant to herbicides that inhibit the enzyme acetohydroxy acid synthase (AHAS, EC 2.2.1.6). AHAS is the first enzyme of the biosynthetic pathway that produces the branched-chain of the essential amino acids valine, leucine, and isoleucine. Therefore, multiple copies of the AHAS gene might be of interest for breeding programs targeting herbicide resistance. In this work, the characterization of the AHAS gene was accomplished for the Chenopodium quinoa Regalona-Baer cultivar. Cloning, sequencing, and Southern blotting were conducted to determine the number of gene copies. Results The presence of multiple copies of the AHAS gene as has been shown previously in several other species is described. Six copies of the AHAS gene were confirmed with Southern blot analyses. CqHAS1 and CqAHAS2 variants showed the highest homology with AHAS mRNA sequences found in the NR Database. A third copy, CqAHAS3, shared similar fragments with both CqAHAS1 and CqAHAS2, suggesting duplication through homeologous chromosomes pairing. Conclusions The presence of multiple copies of the gene AHAS shows that gene duplication is a common feature in polyploid species during evolution. In addition, to our knowledge, this is the first report of the interaction of sub-genomes in quinoa.

Genetic diagnosis for a family without exonic deletions and duplications of dystrophin gene / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To conduct genetic diagnosis for a family in which no exonic deletions and duplications of the dystrophin gene were detected.</p><p><b>METHODS</b>Potential exonic deletions and duplications of the dystrophin gene were initially analyzed with using multiplex ligation-dependent probe amplification (MLPA). Subsequently, all of the 79 exons of the dystrophin gene of the proband and a pregnant woman from the family were analyzed with PCR amplification and DNA sequencing. Following identification of the causative mutation, prenatal diagnosis was provided.</p><p><b>RESULTS</b>MLPA analysis had detected no exonic deletions and duplications of the dystrophin gene. Sequence analysis has identified a C>T mutation on the 22nd nucleotide position of the 70th exon of the dystrophin gene (c.10108 C>T), which has replaced the codon CGA to a stop codon (TGA). The patient's mother and sister were both heterozygous for the same mutation. Upon prenatal diagnosis, the fetus was found to be positive for the Y chromosome sex-determining gene (SRY) and has carried above mutation. The result of short tandem repeat linkage analysis also confirmed that the fetus has inherited the mutant X chromosome.</p><p><b>CONCLUSION</b>The causative mutation of the dystrophin gene has been discovered in an affected family, which has enabled prenatal diagnosis of the disease.</p>

Advance in research on MECP2 corrected duplication syndrome / 中华医学遗传学杂志

Methyl-CpG-binding protein 2 gene (MECP2; OMIM 300005) is located at chromosome Xq28. Mutations of the gene including point mutation, duplication and deletion can lead to severe neurodevelopmental disorders. The disease caused by duplication of the entire MECP2 gene, named as MECP2 duplication syndrome, is mostly seen in males. The clinical manifestation of this syndrome include mental retardation, hypotonia, poor speech development, recurrent infection, progressive spasticity, epilepsy, autism or autistic features with or without midface hypoplasia. Most patients have inherited the duplication from their unaffected mothers, with only a few cases having de novo mutation. Females with duplicated MECP2 gene are typically asymptomatic because of a skewed X chromosome inactivation (XCI) pattern. Proposed mechanisms of this genomic rearrangement include fork stalling and template switching (FoSTeS) and microhomology mediated break-induced replication (MMBIR). Since no effective treatment is available for this disease, proper genetic counseling and prenatal diagnosis for the high risk families are crucial.

Different active ingredients of medicinal plant based on function differentiation of homologous gene / 中国中药杂志

In the research field of quality control in Chinese medicinal materials, variation in active ingredients of medicinal plant is always the key and hot issues. With the development of high-throughput sequencing technologies and reducing cost, a large numbers of genes from medicinal plant were cloning and provide a solid foundation for further research of gene structure and its biological function, and also provides conditions for explore active ingredient variation and its quality control from the perspective of molecular pharmacognosy. This paper introduces the concept of homologous gene, gene duplication and classification. We prospect the function of duplicated genes in the role of molecular mechanism research about variation in active ingredients, aiming at providing a new way for medicinal materials quality control.

[Association of intron 3 16 bp duplication polymorphism of p53 with thyroid cancer in northwest of Iran]

Intron 3 16 bp duplication polymorphism of p53 gene has been associated with increased risk of colorectal, breast and lung cancers. Nevertheless there are inconsistent results and we need more studies to understand the importance of this polymorphism in increased risk of cancer predisposition. The aim of this study was to assess the association of 16 bp duplication polymorphism of p53 with thyroid cancer risk. Material and This case-control study included 105 thyroid patients and 170 controls. Cases and controls were matched for age, sex and ethnicity. Genomic DNA was extracted from peripheral blood samples and tumor tissues. P53 PIN3 genotype was determined using PCR products length analysis on polyacrylamide gel. Result: In the control and case groups, 62.9% and 53.3% had no 16 bp insertion, 7.1% and 8.6% had insertion in both p53 alleles and 30% and 38.1% were heterozygous, respectively. There were no significant differences between the case and control groups in regard to genotype frequencies as well as allelic frequencies. According to the results of our study PIN3 16 bp duplication polymorphism of p53 could not be considered as a risk factor for predisposition to thyroid cancer in northwest of Iran