OBJECTIVETo employ single nucleotide polymorphisms (SNP) microarray to detect copy number variations (CNVs) for the diagnosis of disease and molecular classification.

METHODSFor a patient with split-hand/split-foot malformation, genome-wide copy number variants SNP microarray was applied. Tiny copy number variations were verified by real-time fluorescent quantitative PCR.

RESULTSThe results of SNP microarray has revealed that the patient has carried a 0.39 Mb duplication in 10q24.31-24.32 (102 955 122-103 348 688), which has encompassed genes including LBX1, BTRC and POLL. By real-time fluorescent quantitative PCR, duplicate area encompassing the pathogenic genes have been verified. The results for LBX1, BTRC, POLL genes were all consistent with the SNP microarray test. Moreover, a duplication was detected in exon 9 of FBXW4 gene which is in nearby.

CONCLUSIONSNP chips can efficiently identify tiny CNVs (< 1.0 Mb). In combination with real-time fluorescence quantitative PCR, this may provide valuable information for prenatal diagnosis.

Adult ; Asian Continental Ancestry Group ; genetics ; China ; Chromosome Duplication ; DNA Copy Number Variations ; DNA Polymerase beta ; genetics ; Homeodomain Proteins ; genetics ; Humans ; Limb Deformities, Congenital ; genetics ; Male ; Polymorphism, Single Nucleotide ; Transcription Factors ; genetics ; beta-Transducin Repeat-Containing Proteins ; genetics

OBJECTIVETo analyze deaf-related genes in patients with nonsyndromic hearing loss (NSHL) and set up a prenatal diagnosis system for such patients.

METHODSNine NSHL families were collected. Potential mutations of GJB2 (35delG, 176del16, 235delC, 299delAT), SLC26A4 (2168A> G, IVS7-2A> G), GJB3 (538C> T) and mtDNA (1494C> T, 12S rRNA 1555A> G) were detected by direct sequencing. Maternal blood contamination was excluded prior to the testing.

RESULTSSixteen patients from 4 families were detected with GJB2 mutations, 8 patients from 2 families were found with SLC26A4 mutations, and 4 patients from 2 families were found with mutations in mtDNA. For 2 patients from one remaining family, no mutations were found with above genes.

CONCLUSIONA diagnostic system for NSHL has been established, which may provide a basis for prenatal diagnosis and genetic counseling to NSHL families.

Connexin 26 ; Connexins ; genetics ; DNA Mutational Analysis ; DNA, Mitochondrial ; chemistry ; genetics ; Deafness ; diagnosis ; genetics ; Family Health ; Female ; Genetic Predisposition to Disease ; genetics ; Hearing Loss ; diagnosis ; genetics ; Humans ; Male ; Membrane Transport Proteins ; genetics ; Molecular Sequence Data ; Mutation ; Pedigree ; Pregnancy ; Prenatal Diagnosis ; methods ; RNA, Ribosomal ; genetics ; Reproducibility of Results ; Sensitivity and Specificity

OBJECTIVETo explore the genetic etiology of fetal abnormalities detected by prenatal ultrasound through single nucleotide polymorphism (SNP array) analysis.

METHODSTwo hundred and eight fetuses were tested with SNP array and conventional karyotyping. Complex copy number variations (CNVs) were verified with fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA) and quantitative fluorescence polymerase chain reaction (QF-PCR).

RESULTSFor the 208 cases, the diagnostic yields of conventional karyotping and SNP assay were 8.2%(17/208) and 13.9%(29/208), respectively. For fetuses with malformations of the cardiovascular system, central nervous system or multiple systems, pathogenic CNVs was detected in 4.6% (8/174), 2.3%(4/174), and 1.1% (2/174) of all fetuses, respectively. No pathogenic CNVs was detected among those with abnormalities of the renal system, digestive system, skeletal system, facial dysmorphism or respiratory system.

CONCLUSIONCNVs are significantly related with birth defects. Compared with conventional karyotyping, SNP array is a better platform for CNVs detection and can provide more clues for genetic counseling, recurrence risk assessment and prenatal diagnosis.

Adult ; Chromosome Aberrations ; DNA Copy Number Variations ; Female ; Fetal Diseases ; diagnosis ; diagnostic imaging ; genetics ; Genome-Wide Association Study ; Humans ; Infant, Newborn ; Karyotyping ; Male ; Polymorphism, Single Nucleotide ; Pregnancy ; Pregnancy Complications ; diagnosis ; diagnostic imaging ; genetics ; Prenatal Diagnosis ; Ultrasonography ; Young Adult

OBJECTIVETo establish individualized prenatal diagnosis program for families affected with Duchenne/Becker muscular dystrophy (DMD/BMD) and different clinical background using a variety of methods.

METHODSMultiplex ligation-dependent probe amplification (MLPA) was performed on 50 patients suspected for DMD/BMD. For single exon deletions of the DMD gene, PCR was used for validating the results. For those without any deletion or duplication, Sanger sequencing was used to screen for DMD gene mutations in the children and their mothers. Prenatal genetic testing was provided to female carriers using chorionic villus, amniocentesis or cord blood samples. To ensure the accuracy of diagnosis, all prenatal specimens were also subjected to linkage analysis.

RESULTSAmong the 50 patients with DMD/BMD, 23 harbored large deletions, 11 only had single exon deletions, 10 harbored duplications, and 5 had small scare mutations. No mutation was detected in one family. For 37 women undergoing prenatal diagnosis, 10 fetuses were identified as affected males, 6 were female carriers, while 21 were not found to carry any mutation. Testing of creatine kinase was consistent with the results of prenatal diagnosis. For a patient harboring exon 51 deletion, the same mutation was found in a fetus but not in their mother. The proband and fetus had inherited the same haplotype, which suggested that the mother probably has germline mosaicism for the mutation.

CONCLUSIONApplication of individualized methods for analyzing pregnant women with different clinical background can minimize the risk for giving birth to further children affected with DMD/BMD.

Adolescent ; Child ; Child, Preschool ; DNA Mutational Analysis ; Exons ; Female ; Humans ; Male ; Multiplex Polymerase Chain Reaction ; Muscular Dystrophy, Duchenne ; diagnosis ; genetics ; Mutation ; Pedigree ; Pregnancy ; Prenatal Diagnosis

Serum vitamin D level and vitamin D receptor (VDR) gene FokI polymorphisms were detected in 200 single full-term pregnant women who gave birth in our hospital during 2016 to 2018. The newborns with birth weight<2500 g were diagnosed as fetal growth restriction (FGR), there were 100 cases in FGR group and 100 cases in control group. The average level of vitamin D in pregnant women in FGR group was significantly lower than that of the control group [(30.1±10.9) vs. (36.1±15.8) nmol/L, P<0.05]. In the FGR group, the birth weight of infants in mother carrying ff genotype was significantly lower than that in mother carrying Ff and FF genotypes [(2073±90) g vs. (2242±122) g and (2349±96) g, P<0.05]. Pregnant women carrying Ff and FF genotypes had lower risk of FGR than those of carrying ff genotype (ORFf=0.31, 95％ CI: 0.17-0.76; ORFF=0.28, 95％CI: 0.11-0.46). The pregnant women with serum 25(OH)D level>30 nmol/L carrying F allele (FF+Ff) were set as reference, the risk of FGR in pregnant women with serum 25 (OH)D level ≤ 30 nmol/L carrying ff genotype was increased (OR=6.14, 95％CI: 2.13-13.23). The polymorphism of VDR gene FokI may be associated with the occurrence of FGR. In the case of vitamin D deficiency, the influence of ff genotype on FGR is more tangible.

OBJECTIVE: To carry out mutation analysis for a Chinese family affected with autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS). METHODS: Whole exome sequencing (WES) was used to screen potential mutations within genomic DNA extracted from the proband. Suspected mutation was validated by combining clinical data and results of Sanger sequencing. RESULTS: A homozygous deletional mutation c.3665_3675delGTGCTGTCTTA (p.S1222fs) was found in the proband, for which her parents were both heterozygous carriers. CONCLUSION WES is capable of detecting mutation underlying this disorder and facilitating genetic counseling and prenatal diagnosis for the affected family. A novel pathogenic mutation of the SACS gene was discovered.
Female ; Genes, Recessive ; Heat-Shock Proteins ; genetics ; Humans ; Muscle Spasticity ; Mutation ; Spinocerebellar Ataxias ; congenital

OBJECTIVE: To explore the genetic etiology of two patients with Perrault syndrome (PRLTS) in a family. METHODS: Whole exome sequencing (WES) was carried out to screen potential variants within genomic DNA extracted from the proband. Suspected variants were validated by clinical data and results of Sanger sequencing. RESULTS: WES has identified two heterozygous variants of TWNK gene, namely c.1172G>A (p.Arg391His) and c.1844G>C (p.Gly615Ala). Sanger sequencing confirmed that the c.1172G>A (p.Arg391His), a known pathogenic variant, was derived from her father, while the c.1844G>C (p.Gly615Ala), a novel variant, was derived from her mother. Her brother, who was similarly affected, has carried the same compound heterozygous variants. CONCLUSION The compound heterozygous variants c.1172G>A (p.Arg391His) and c.1844G>C (p.Gly615Ala) of the TWNK gene probably underlie PRLTS in the sib pair. The above results have facilitated genetic counseling and prenatal diagnosis for the affected family.

OBJECTIVE: To explore the genetic variation of a Chinese family affected with congenital insensitivity to pain with anhidrosis and albinism. METHODS: Whole exome sequencing (WES) was carried out to screen potential variants within genomic DNA extracted from the proband and his parents. Whole genome sequencing (WGS) was applied when variants were not found completely. Suspected variants were validated by Sanger sequencing. RESULTS: WES has identified a heterozygous c.1729G>C (p.G577R) variant of NTRK1 gene and two heterozygous variants of OCA2 gene, namely c.1363A>G (p.R455G) and c.1182+1G>A. WGS has identified two additional heterozygous variants c.(851-798C>T; 851-794C>G) in deep intronic regions of the NTRK1 gene. CONCLUSION The compound heterozygous variants of the NTRK1 gene probably underlay the congenital insensitivity to pain with anhidrosis. And the compound heterozygous variants of the OCA2 gene probably underlay the albinism in the proband. In the case where no variant is detected by WES in the coding region, WGS should be considered to screen potential variants in the whole genome.
Albinism ; Child ; DNA Mutational Analysis ; Hereditary Sensory and Autonomic Neuropathies/genetics* ; Heterozygote ; Humans ; Membrane Transport Proteins ; Mutation ; Pedigree

OBJECTIVETo explore the clinical characteristics and genetic mutation in a family affected with hypophosphatemic rickets.

METHODSWhole exome sequencing (WES) was used to screen potential mutations in genomic DNA extracted from peripheral venous blood sample from the proband. Suspected mutation was confirmed with Sanger sequencing. Amniotic fluid was sampled from the proband for prenatal diagnosis. Potential maternal contamination was excluded by analysis of short tandem repeat (STR) markers.

RESULTSWES has identified a heterozygous c.2058_2059insAGTT (p.L686fs) mutation of the PHEX gene in the proband, which was confirmed by Sanger sequencing in other affected individuals from the family. The mutation was detected in the amniotic fluid sample from the fetus but not among healthy members from the family.

CONCLUSIONIdentification of the PHEX mutation by WES has facilitated genetic counseling and prenatal diagnosis for the family affected with hypophosphatemic rickets.

Adult ; DNA Mutational Analysis ; Exome ; Familial Hypophosphatemic Rickets ; diagnosis ; genetics ; Female ; Humans ; Microsatellite Repeats ; Mutation ; PHEX Phosphate Regulating Neutral Endopeptidase ; genetics ; Pregnancy ; Prenatal Diagnosis ; Whole Genome Sequencing

OBJECTIVETo analyze PKHD1 gene mutation in a family affected with autosomal recessive polycystic kidney disease (ARPKD).

METHODSGenomic DNA was extracted from peripheral and cord blood samples obtained from the parents and the fetus. Potential mutations were identified using targeted exome sequencing and confirmed by Sanger sequencing. Pathogenicity of the mutation was analyzed using PolyPhen-2 and SIFT software.

RESULTSCompound heterozygous mutations of c.11314C>T (p.Arg3772*) and a novel missense c.889T>A (p.Cys297Ser) of the PKHD1 gene were identified in the fetus. The mother was found to have carried the c.11314C>T mutation, while the father was found to have carried the c.889T>A mutation. PolyPhen-2 and SIFT predicted that the c.889T>A mutation is probably damaging.

CONCLUSIONA novel mutation in PKHD1 gene was detected in our ARPKD family. Compound heterozygous PKHD1 mutations were elucidated to be the molecular basis for the fetus affected with ARPKD, which has facilitated genetic counseling and implement of prenatal diagnosis for the family.

Abortion, Eugenic ; Adult ; Amino Acid Sequence ; Base Sequence ; DNA Mutational Analysis ; Family Health ; Fatal Outcome ; Female ; Fetal Diseases ; diagnostic imaging ; genetics ; Fetus ; abnormalities ; metabolism ; Humans ; Male ; Mutation ; Polycystic Kidney, Autosomal Recessive ; diagnostic imaging ; embryology ; genetics ; Pregnancy ; Receptors, Cell Surface ; genetics ; Sequence Homology, Amino Acid ; Ultrasonography, Prenatal ; methods