Identification of pathogenic variant and preimplantation genetic testing for a Chinese family affected with osteogenesis imperfecta / 中华医学遗传学杂志

OBJECTIVE@#To identify the pathogenic variant for a husband with osteogenesis imperfecta and provide preimplantation genetic testing (PGT) for the couple.@*METHODS@#High-throughput sequencing and Sanger sequencing were carried out to identify the pathologic variant in the husband patients. PGT of embryos was performed through direct detection of the mutation site. Meanwhile, chromosome aneuploidy of the blastocysts was screened. Following transplantation, cytogenetic and genetic testing of fetal amniotic fluid sample was carried out during mid-pregnancy. Chromosome copy number variant (CNV) was detected at multiple sites of the placenta after delivery.@*RESULTS@#The husband was found to harbor heterozygous c.544-2A>G variant of the COL1A1 gene. The same variant was not detected in either of his parents. PGT revealed that out of three embryos of the couple, one was wild-type for the c.544-2A site but mosaicism for duplication of 16p13.3.11.2. The other two embryos were both heterozygous for the c.544-2A>G variant. Following adequate genetic counseling, the wild-type embryo was transplanted. Amniotic fluid testing confirmed that the fetus had normal chromosomes and did not carry the c.544-2A>G variant. The copy number of chromosomes at different parts of placenta was normal after birth.@*CONCLUSION@#For couples affected with monogenic disorders, e.g., osteogenesis imperfecta, direct detection of the mutation site may be used for PGT after identifying the pathogenic variant. After adequate genetic counseling, prenatal diagnosis must be carried out to ensure the result.

Preliminary study on the application of third-generation sequencing technology for the detection of chromosomal aneuploidies / 中华医学遗传学杂志

OBJECTIVE@#To apply nanopore third-generation sequencing for the detection of chromosomal aneuploidy samples, and explore its performance and application prospects.@*METHODS@#DNA extracted from two human cell lines with X chromosome monosomy and 22.5 Mb deletion in 7q11.23-q21.3 region was sequenced with a MinION sequencer, and the results were analyzed.@*RESULTS@#Respectively, 555 872 and 2 679 882 reads were obtained from the two samples within 24 hours, with genome coverage being 53.75% and 88.63%. With a sequencing depth of 0.81× and 2.40× , respectively, the abnormal chromosomal regions could be detected by comparative analysis using Minimap2.@*CONCLUSION@#With low-depth whole genome sequencing, the use of nanopore third-generation sequencing is expected to complete the detection and analysis of chromosomal aneuploidy samples within 24 hours, but its further application and promotion needs to overcome the cost constraints.

Clinical manifestation and genetic analysis of a child with early infantile epileptic encephalopathy 42 / 中华医学遗传学杂志

OBJECTIVE@#To analyze the clinical phenotype and genetic characterization of a child with early infantile epileptic encephalopathy.@*METHODS@#The proband was subjected to history taking and was diagnosed based on his clinical manifestation, magnetic resonance imaging (MRI) and whole exome sequencing (WES). Sanger sequencing was carried out to determine the origin of pathogenic variant.@*RESULTS@#The proband unconsciously tilts his head to one side with squint, which revealed an abnormal discharge. MRI indicated suspicious abnormal signal shadow in the left posterior frontal cortex in addition with inflammation signs in the right maxillary sinus and ethmoid sinus. WES revealed that the proband has carried a heterozygous c.5789G>A variant in the CACNAIA gene. The result of Sanger sequencing was in keeping with that of WES. Neither of his parents has carried the same variant.@*CONCLUSION@#The heterozygous c.5789G>A variant of the CACNAIA gene probably underlay the early infantile epileptic encephalopathy 42 in the proband, which has a de novo origin.

Phenotypic and mutation analysis of a fetus with Cornelia de Lange syndrome Ⅰ / 中华医学遗传学杂志

OBJECTIVE@#To carry out genetic testing for an abortus suspected with Cornelia de Lange syndrome (CdLS).@*METHODS@#History of gestation and the family was taken. Combined with prenatal ultrasonography and the phenotype of the abortus, a diagnosis was made for the proband. Fetal tissue and peripheral blood samples of its parents were collected for the extraction of genomic DNA. Whole exome sequencing was carried out to detect mutations related to the phenotype. Suspected mutations were verified in the parents through Sanger sequencing.@*RESULTS@#Prenatal ultrasound found that the forearms and hands of the fetus were anomalous, in addition with poorly formed vermis cerebellum, slight micrognathia, and increased echo of bilateral renal parenchyma. Examination of the abortus has noted upper limb and facial malformations. Whole exome sequencing revealed that the fetus carried a heterozygous c.2118delG (p.Lys706fs) frameshift mutation of the NIPBL gene. The same mutation was not found in either parent.@*CONCLUSION@#The heterozygous c.2118delG (p.Lys706fs) frameshift mutation of the NIPBL gene probably underlies the CdLS in the fetus. Above finding has provided a basis for the genetic counseling for the family.

A review on the status quo and implementation methods of ethics education in standardized training for resident doctors in medical genetics department / 中华医学遗传学杂志

Clinical practice of Medical Genetics involves application of various genetic techniques for the diagnosis of genetic disorders and subsequent genetic counseling and treatment. The principles of Medical Ethics must be fully taken into account when applying genetic knowledge for medical practice. Medical Ethics education is therefore essential for the standardized training of resident doctors in medical genetics department. With a basic system of Medical Genetics Physician Training established, our hospital has made a preliminary exploration for the development of Medical Ethics teaching in resident training through various teaching practices including seminar, network teaching, case study, scene teaching and outpatient teaching, with an aim to strengthen Medical Ethnics knowledge, professionalism and communication skills, and implement Medical Ethics principles throughout clinical practice.

Application of single sperm sequencing for preimplantation genetic testing of male patient with achondroplasia / 中华医学遗传学杂志

OBJECTIVE@#To assess the value of single sperm sequencing in preimplantation genetic diagnosis.@*METHODS@#A male patient with achondroplasia due to a de novo FGFR3 variant was subjected to single sperm isolation and sequencing. Twenty single sperm samples were isolated by mechanical immobilization, and their whole genome was amplified. PCR primers were designed for the variant site and 25 flanking single nucleotide polymorphism (SNP) loci, and the PCR products were sequenced to determine the chromosomal haplotype which did not harbor the pathogenic variant. Biopsy samples of 12 embryonic trophoblasts were taken. Following whole genome amplification, high-throughput sequencing was carried out to detect the carrier status of the embryos. Wild type blastocysts were selected for transplantation. Amniotic fluid samples were taken at 19 weeks of gestation to confirm the status of the fetus.@*RESULTS@#Eight SNP were selected by single sperm sequencing, with which the haplotypes were successfully constructed. Preimplantation genetic testing indicated that 5 embryos have carried the pathogenic variant and 7 did not. Testing of amniotic fluid sample during the second trimester of pregnancy confirmed that the fetus did not carry the FGFR3 gene c.1138G>A variant.@*CONCLUSION@#For male patients carrying de novo pathogenic variants, SNP sites can be selected through single sperm sequencing, and haplotypes can be constructed by linkage analysis for preimplantation genetic diagnosis.

Clinical feature and pathogenic analysis of a fetus with split hand-foot malformation / 中华医学遗传学杂志

OBJECTIVE@#To analyze the clinical feature of a fetus with split hand-foot malformation (SHFM) and to explore its etiology.@*METHODS@#Ultrasonographic finding of the fetus and X-ray examination of the abortus were reviewed. Genomic copy number variations (CNVs) of the fetus was analyzed by next-generation sequencing (NGS). Its parents were subjected to chromosomal karyotyping, NGS and fluorescence in situ hybridization (FISH) assays. Real-time fluorescence quantitative PCR was used to measure the expression of genes from the region containing abnormal CNVs.@*RESULTS@#Ultrasonography and X-ray revealed that the right hand and both feet of the fetus were in a V-shape, which was suggestive of SFHM. The results of NGS revealed that the fetus has carried a 0.36 Mb deletion at 7q21.3 region. FISH and NGS analysis of both parents were normal. Real-time fluorescence quantitative PCR confirmed that the fetus carried a single copy of DYNC1I1 gene, while the copy numbers of SEM1, DLX5 and DLX6 genes were normal.@*CONCLUSION@#The 7q21.3 microdeletion probably underlies the SHFM of the fetus, which has a de novo origin.

Phenotype-genotype analysis and detection of gene variant in six families with osteogenesis imperfecta / 中华医学遗传学杂志

OBJECTIVE@#To analyze the clinical phenotype of six pedigrees affected with osteogenesis imperfecta and their genetic basis.@*METHODS@#Peripheral blood or abortic tissues of the six pedigrees were collected for the extraction of genomic DNA. Next generation sequencing (NGS) was carried out to detect pathological variants in the genome. Sanger sequencing was used for validating suspected variant among the six pedigrees and 100 healthy controls.@*RESULTS@#In pedigree 1, the proband and his daughter both carried a heterozygous c.1976G>C variant of COL1A1. The probands in pedigrees 2 to 6 respectively carried heterozygous variants of c.2224G>A of COL1A2, c.2533G>A of COL1A1, c.2845G>A of COL1A2, c.2532_2540del of COL1A1, and c.1847G>A of COL1A2. The same variants were not detected in their parents and the 100 healthy controls.@*CONCLUSION@#Variants of COL1A1/2 gene probably underlie the pathogenesis for osteogenesis imperfecta in these pedigrees. Discovery of the nevol variants has enriched the spectrum of COL1A1/2 gene variants and facilitated genetic counseling and prenatal diagnosis for the affected pedigrees.

Clinical features and genetic analysis of a fetus with holoprosencephaly / 中华医学遗传学杂志

OBJECTIVE@#To analyze the clinical features and pathogenesis of a fetus with holoprosencephaly.@*METHODS@#The findings of prenatal ultrasonography was reviewed. Following elective abortion, whole exome sequencing (WES) was carried out to identify potential pathogenic variant. Copy number variants (CNVs) of the abortus and its parents were detected by low-depth high-throughput sequencing. The parents were also analyzed by chromosomal karyotyping.@*RESULTS@#Prenatal ultrasound suggested that the fetus had holoprosencephaly. WES revealed that it had approximately 33 Mb deletion at chromosome 13 involving ZIC2, a haploid dose sensitive gene. The results of low-depth high-throughput sequencing confirmed that the fetus carried a de novo 32.32 Mb deletion at 13q31.1-34. Karyotyping analysis has excluded gross chromosomal aberration in both parents.@*CONCLUSION@#The fetus was diagnosed with holoprosencephaly, which may be attributable to the 13q31.1-34 deletion involving the ZIC2 gene.

Genetic analysis of three fetusesaffected with cardiac rhabdomyomas / 中华医学遗传学杂志

OBJECTIVE@#To report on echocardiographic finding and genetic testing of three fetuses with cardiac rhabdomyoma.@*METHODS@#Clinical data of the three fetuses was collected. High-throughput sequencing was carried out to analyze the whole exomes of the three fetuses. Suspected variants were confirmed by Sanger sequencing.@*RESULTS@#Multiple hyperechoic masses were found in both ventricles of the three fetuses, suggesting the presence of fetal cardiac rhabdomyoma. Genetic testing revealed that fetus 1 carried a heterozygous c.740G>A (p.W247*) variant of the TSC1 gene, fetus 2 carried a previously known heterozygous c.3352C>T (p.Q1118*) variant of the TSC2 gene. Fetus 3 carried a previously known heterozygous c.1579C>T (p.Q527*) variant of the TSC1 gene. None of their parents carried the same variant. Literature review has identified 109 fetuses with relatively complete data. Cardiac rhabdomyomas in ventricles and ventricular septum was reported in 89, and multiple cardiac rhabdomyoma was reported in 79. Out of the 94 cases who underwent genetic testing, 74 have carried variants of the TSC1 or TSC2 genes.@*CONCLUSION@#Fetal cardiac rhabdomyoma may present as multiple hyperechoic intraventricular masses. Most of them are associated with other manifestation of tuberous sclerosis. Such cases may warrant prenatal genetic testing.

Diagnosis of a fetus with atelosteogenesis type 2 through combined prenatal ultrasonography and whole exome sequencing / 中华医学遗传学杂志

OBJECTIVE@#To explore the genetic basis for fetus with short limbs detected by prenatal ultrasonography.@*METHODS@#Results of clinical imaging of the fetus was collected. Amniotic fluid sample was collected through amniocentesis for the extraction of fetal DNA. Whole exome sequencing was carried out to detect variants related to the clinical phenotypes. Candidate variant was verified by Sanger sequencing.@*RESULTS@#Prenatal ultrasound showed that the fetus had short limbs but no other abnormality. Whole exome sequencing has identified that the fetus carried two heterozygous pathogenic variants c.484G>T and c.1436dupA of the SLC26A2 gene, for which its mother and father were heterozygous carriers, respectively.@*CONCLUSION@#The fetus was diagnosed with atelosteogenesis type 2 by combined prenatal ultrasonography and whole exome sequencing, which may be attributed to the compound heterozygous variants of the SLC26A2 gene. Above findings provided evidence for the diagnosis of the fetus and genetic counseling.

Analysis of prenatal phenotype and pathogenetic variant in a fetus with Papillorenal syndrome / 中华医学遗传学杂志

OBJECTIVE@#To diagnose a fetus with Papillorenal syndrome by prenatal ultrasonography and genetic testing, and to correlate its genotype with phenotype.@*METHODS@#Ultrasound finding of the fetus was reviewed. Muscle sample of the abortus was taken, and genetic variant related to the clinical phenotype was screened by whole exome sequencing (WES). Suspected pathogenic variant was verified by Sanger sequencing.@*RESULTS@#Prenatal ultrasound revealed severe dysplasia of the fetal kidneys and oligohydramnios. WES revealed that the fetus has carried a c.736G>T (p.Glu246Ter) nonsense variant of the PAX2 gene, which was unreported previously. The result of Sanger sequencing was consistent with that of WES. Both parents of the fetus were of the wild-type, suggesting a de novo origin of the fetal variant.@*CONCLUSION@#The novel heterozygous c.736G>T (p.Glu246Ter) variant of the PAX2 gene probably underlay the Papillorenal syndrome in the fetus. Above finding has provided a basis for genetic counseling and clinical decision-making.

Mutation analysis in a large Chinese pedigree affected with preaxial polydactyly II / 中华医学遗传学杂志

OBJECTIVE@#To detect potential mutation in a large pedigree affected with preaxial polydactyly II.@*METHODS@#With informed consent obtained, peripheral blood samples were collected from the proband, her family members as well as 100 healthy controls. Genomic DNA was extracted. The zone of polarizing activity regulatory sequence (ZRS) of the SHH gene was amplified by PCR and subjected to bi-directional Sanger sequencing.@*RESULTS@#The pedigree had typical preaxial polydactyly II. A heterozygous C>G mutation at position 105 of the ZRS region was detected in all patients but none of the unaffected members and 100 healthy controls.@*CONCLUSION@#The heterozygous 105C>G mutation of the ZRS region probably underlies the disease in this pedigree.

Phenotypic and genetic analysis of a pedigree with 4p16 microduplication and 8p23 microdeletion / 中华医学遗传学杂志

Objective@#To explore the nature and origin of chromosomal copy number variants (CNVs) in a pedigree affected with mental retardation.@*Methods@#Genomic CNVs of the proband were analyzed by next generation sequencing (NGS). Chromosomal karyotypes of the proband and his relatives were analyzed with high-resolution karyotyping and fluorescence in situ hybridization (FISH).@*Results@#Clinical phenotypes of the proband and other patients from the pedigree included mental retardation and mild dysmorphism. The results of NGS revealed that the proband carried a 16.24 Mb microduplication at 4p16.3-15.32 and a 2.2 Mb microdeletion at 8p23.3-23.2. Other patients of the pedigree harbored the same variants, while those without the phenotypes did not harbor the variants. The results of high-resolution karyotyping and FISH revealed that the mother of the proband carried a reciprocal translocation between 4p and 8p, and her karyotype was 46, XX, t(4; 8)(p16; p23). No karyotypic abnormality was detected in his father.@*Conclusion@#The abnormal phenotypes of this pedigree may be attributed to 4p microduplication in conjunct with 8p microdeletion derived from a maternal balanced translocation between 4p and 8p.

Identification of a novel GPR143 mutation in a Chinese family affected with X-linked ocular albinism / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To detect mutation of GPR143 gene in a Chinese patient affected with ocular albinism.</p><p><b>METHODS</b>Peripheral blood samples were collected from the proband and his parents. The coding regions of the GPR143 gene were subjected to PCR amplification and Sanger sequencing.</p><p><b>RESULTS</b>A previously unreported mutation (c.758T>A) was found in exon 6 of the GPR143 gene in the proband and his mother. The same mutation was not found in his father. As predicted, the mutation has resulted in a stop codon, causing premature termination of protein translation.</p><p><b>CONCLUSION</b>A novel mutation of the GPR143 gene related to X-linked ocular albinism has been identified.</p>

Analysis of genomic copy number variations in 36 fetuses with heart malformations using next-generation sequencing / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To explore the implications of copy number variations (CNVs) for congenital heart diseases (CHD) in fetuses.</p><p><b>METHODS</b>G-banding karyotype analysis and next-generation sequencing (NGS) technology were performed on cord blood samples derived from 36 fetuses with CHD. Pathological implication of the CNVs was explored through comparison against the International Genomic Polymorphism Database (http://www.ebi.ac.uk/dgva/), Phenotype Database (http://decipher.sanger.ac.uk/), and the Human Genome Database at UCSC (http://genome.ucsc.edu/cgi-bin/hgGateway).</p><p><b>RESULTS</b>G-banding karyotype analysis has identified 7 chromosomal abnormalities. For the remaining 28 cases, NGS has identified 4 microdeletions and microduplications, which involved chromosomes 2, 13, 14, 16 and 22. The largest involved a 6.8 Mb microdeletion, while the smallest involved a 280 kb microduplication. The chromosomal breakpoints in 1 case were delineated. One case of Noonan syndrome and one case of 22q11.2 deletion were diagnosed.</p><p><b>CONCLUSION</b>NGS can accurately determine the origins of derivative chromosomes and facilitate identification of pathogenic CNVs/genes. It can serve as a useful complement for conventional G-banding and reduce the recurrence risk.</p>

Genetic diagnosis and follow up of a fetus with Emanuel syndrome / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To carry out genetic analysis for a fetus with Dandy-Walker malformation and provide prenatal diagnosis for its parents during the subsequent pregnancy.</p><p><b>METHODS</b>Routine G-banding was carried out to analyze the karyotype of the fetus and its parents, and next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) were used to verify the result.</p><p><b>RESULTS</b>The father showed a normal karyotype, while the mother was found to carry a balanced t(11; 22) (q23; q11) translocation. NGS and FISH analysis verified that the supernumerary marker chromosome carried by the fetus was der(22) t(11; 22) (q23;q11). The fetus was diagnosed with Emanuel syndrome. During the next pregnancy, the fetus was found to carry the same balanced translocation as its mother. After genetic counseling, the couple decided to continue with the pregnancy, and eventually delivered a healthy baby.</p><p><b>CONCLUSION</b>A fetal case of Emanuel syndrome has been identified. The derivative der(22) t(11; 22)(q23; q11) chromosome probably underlies the Dandy-Walker malformation in the fetus. Combined cytogenetic and molecular analyses can attain a more precise diagnosis for fetal abnormalities detected by ultrasonography.</p>

Influence of genetic polymorphisms and non-genetic factors on the maintenance dose of warfarin / 中华医学遗传学杂志

OBJECTIVE To assess the influence of genetic polymorphisms and non-genetic factors on warfarin maintenance dose variations in order to provide guidance for personalized use of warfarin. METHODS Two hundred patients from outpatient and inpatient with stable international normalized ratio(INR) were recruited. Clinical data and blood samples were collected. Genotypes of 4 genes involved in warfarin metabolic pathways were determined with Sanger sequencing. Based on statistical analysis of warfarin maintenance dosage, a mathematical model was established. RESULTS Among non-genetic factors, the age and height have significant influence in warfarin dosage. The dosage is negatively correlated with age but positively correlated with height. The difference in dosage for between the 20-year-old group and 60-year-old group has reached 1.81 mg/day, and that for between the 140 cm in height and 180 cm in height groups has reached 1.06 mg/day. VKORC1 -1639G/A, CYP2C9 430C/T, CYP2C9 1075A/C and CYP4F2 V433M polymorphisms have significant influence on stable warfarin dosage. The dosage for patients with wild type and mutant genotypes has varied from 0.35 mg/day to 0.84 mg/day. CONCLUSION Non-genetic factors and genetic polymorphisms play important roles in personalized variations of warfarin maintenance dose. The establishment of mathematical models considering multiple factors is helpful in evaluating the safety and effectiveness of warfarin dosage.

Genetic analysis of genitourinary malformations / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To analyze the expression of genes from chromosomal region 22q11.2 and assess the association between mutation(s) of particular gene(s) from this region and malformations of the urinary system.</p><p><b>METHODS</b>Expression of rat homologs of 33 genes from above region was determined in kidney tissues derived from rats of different fetal development ages (E13, E15, E19) and adulthood with reverse transcriptase-PCR. Potential mutation(s) in candidate gene SNAP29, whose expression pattern appeared to be unique, was screened in 44 patients and 220 normal controls with PCR-single strand conformation polymorphism (SSCP). Suspected positive regions were sequenced to verify the mutations.</p><p><b>RESULTS</b>Nine genes showed no expression throughout the whole development process; 18 genes with various expression levels showed continuous expression from the beginning of development; 6 genes only expressed for a short time, among which SNAP29 was selected for mutation screening. Upon sequencing, three mutations were identified from the 44 patients, including a G to A transition (GAG to AAG) in exon 2, and two A to G transitions (AGC to GGC) in exon 3.</p><p><b>CONCLUSION</b>Through systematic analysis of the expression of genes from chromosomal region 22q11.2, the SNAP29 gene was found to have a potential role in the development of genitourinary system. Two missense mutations were identified in three patients. These included one in exon 2 (featuring cryptorchidism), and the other in exon 3 (featuring cryptorchidism and hypospadia). Neither of the mutations was found in the normal controls. The results suggested that mutation(s) of gene(s) from chromosomal region 22q11.2 may play an important role in the genesis of genitourinary malformations.</p>

Another grey zone for clinical genetics: chromosomal microduplication 22q11.2 / 中华医学遗传学杂志

Theoretically, microduplication of chromosomal region 22q11.2, which is rich in segmental duplications, should be as frequent as microdeletions of the same region. Preliminary analysis on the rarity of reports for 22q11.2 microduplication in the literature has suggested that, for the discovery of 22q11.2 microduplication, there has been a lack of sensitivity for routine diagnostic techniques such as karyotyping, PCR and FISH. On the other hand, the diverse anomalies and extremely variable phenotypes of carriers also implied great difficulties one has to face upon clinical consultation. Genetics as well as clinical problems in connection with 22q11.2 microduplication has vividly illustrated the great challenge for the interpretation of genotype-phenotype correlation, and thereby posed yet another gray zone for clinical genetics research.