OBJECTIVETo assess the accuracy of copy number variations (CNVs) detection by non-invasive prenatal testing (NIPT) in addition to its routine targets and clinical significance of such CNVs for the reduction of fetuses born with chromosomal microdeletion/duplication syndromes.

METHODSFrom October 2014 to October 2015, 14 235 pregnant women volunteered to participate in the study. Fifteen cases detected with chromosomal CNVs by the NIPT decided to undergo prenatal diagnostic procedures including amniocentesis, G-banded karyotyping and chromosomal microarray analysis (CMA). All such cases were routinely followed up after birth.

RESULTSAmong the 14 235 subjects underwent NIPT, 18 cases were detected with Down syndrome, 4 with trisomy 18, and 2 with trisomy 13, in addition with 24 cases of CNVs. For the latter, 15 (including 11 cases with microdeletions and 4 cases with microduplications) participated in further prenatal diagnosis. In 13 cases (86.7%), the results of CMA were consistent with those of NIPT. On the other hand, only 7 out of the 15 cases showed a positive result with karyotyping, suggesting a rather high rate of missed diagnosis (46.2%). Of note, karyotyping has identified partial inversion of chromosome 9 in one case.

CONCLUSIONAs a screening tool, NIPT has a high accuracy for the detection of CNVs. However, as this method is still under improvement, it is more of a reminder rather than a diagnostic tool with full capability.

Adolescent ; Adult ; Child ; Child, Preschool ; Chromosome Aberrations ; Chromosome Banding ; Chromosome Disorders ; diagnosis ; embryology ; genetics ; DNA Copy Number Variations ; Female ; Fetal Diseases ; diagnosis ; genetics ; Humans ; Infant ; Infant, Newborn ; Karyotyping ; Male ; Microarray Analysis ; Pregnancy ; Prenatal Diagnosis ; Young Adult

OBJECTIVETo analyze the outcome of chromosomal microarray analysis (CMA) in prenatal diagnosis for fetal abnormalities detected by ultrasonography.

METHODSAmniotic fluid samples from 477 pregnancies with abnormal ultrasound findings but without common aneuploidies were detected by CMA with Affymetrix CytoScan 750K arrays. The results were analyzed with ChAS v3.0 software.

RESULTSAmong the 477 samples, 24 (5.03%) were detected with pathogenic copy number variations (pCNVs) by CMA. Six (9.68%) among 62 cases with structural fetal abnormalities in multiple organ systems were detected with pCNVs, 11 (7.48%) among 147 cases with a single structural anomaly were detected with pCNVs, and 7 (2.61%) among 268 cases with a soft marker were detected with pCNVs.

CONCLUSIONCMA has offered a clear advantage over conventional karyotyping for the detection of fetal chromosomal abnormalities, and can provide an effective diagnostic tool for those with one or more structural abnormalities detected by ultrasound.

Adolescent ; Chromosome Aberrations ; Chromosome Disorders ; diagnosis ; embryology ; genetics ; DNA Copy Number Variations ; Female ; Fetal Diseases ; diagnosis ; diagnostic imaging ; genetics ; Fetus ; diagnostic imaging ; Humans ; Karyotyping ; Male ; Microarray Analysis ; methods ; Pregnancy ; Prenatal Diagnosis ; Ultrasonography, Prenatal ; methods ; Young Adult

OBJECTIVETo explore the application of combined techniques for the prenatal diagnosis of a case with 7q11.23 duplication.

METHODSAmniocentesis was performed in the second trimester for a mother with a high risk suggested by serological prenatal screening. G-banded chromosomal analysis was performed on cultured amniocytes and peripheral blood samples from both parents. DNA from amniotic fluid sample was isolated for a BACs-on-Beads (BoBs) assay. To define the range of duplication, copy number variation was determined with single nucleotide polymorphism array (SNP array, Affymetrix CytoScan 750K) and fluorescence in situ hybridization (FISH) analysis.

RESULTSChromosomal analysis suggested that the fetus and both parents all had a normal karyotype, while a duplication of 7q11.23 was detected by the BoBs assay. SNP array revealed a 1.5 Mb duplication in chromosome 7q11.23, which was confirmed by FISH.

CONCLUSIONCombined prenatal BoBs, SNP array and FISH has enabled effective diagnose of a case with 7q11.23 syndrome.

Adult ; Chromosome Banding ; Chromosome Disorders ; diagnosis ; embryology ; genetics ; Chromosomes, Human, Pair 7 ; genetics ; Female ; Fetal Diseases ; diagnosis ; genetics ; Humans ; Male ; Middle Aged ; Pregnancy ; Prenatal Diagnosis ; Trisomy ; genetics

OBJECTIVETo explore the origin and mechanism of small supernumerary marker chromosomes (sSMC) in order to facilitate genetic counseling.

METHODSChromosome karyotypes of two fetuses and their immediate family members were analyzed by conventional G banding. High-throughput whole genome sequencing was used to determine the origin of sSMCs.

RESULTSFetus 1 was shown to have a karyotype of 47,XY,+mar but with normal FISH and B ultrasound findings. Its father also had a 47,XY,+mar karyotype with normal FISH results and clinical phenotype. High-throughput genome sequencing revealed that fetus 1 and its father were both 46,XY,dup(21)(q11.2;q21.1) with a 6.2 Mb duplication of the long arm of chromosome 21. The fetus was born with normal phenotype and developed well. Its grandmother also had a karyotype of 46,XX,t(15;21)(q13;p13) with normal FISH result and clinical phenotype. The karyotypes of its mother and grandfather were both normal. Analysis of fetus 2 showed a 47,XY,+mar karyotype with normal FISH results. High-throughput genome sequencing suggested a molecular karyotype of 46,XX. The fetus was born with normal phenotype and developed well. The karyotypes of its parents were both normal.

CONCLUSIONConsidering their variable origins, identification of sSMC should combine conventional G banding analyses with high-throughput whole genome sequencing for precise delineation of the chromosomes.

Adult ; Amniotic Fluid ; chemistry ; Chromosome Banding ; Chromosome Disorders ; diagnosis ; embryology ; genetics ; Cytogenetics ; Female ; Fetal Diseases ; diagnosis ; genetics ; Genetic Markers ; Humans ; In Situ Hybridization, Fluorescence ; Infant, Newborn ; Karyotyping ; Male ; Pregnancy ; Prenatal Diagnosis ; Young Adult

OBJECTIVETo explore the rules for free fetal DNA clearance after delivery of fetuses carrying chromosomal aneuploidies.

METHODSFor 10 women carrying 18-to-25-gestation-week singletons confirmed to have chromosomal abnormalities by amniotic karyotyping, 5 mL of peripheral venous blood was drawn respectively before and 15 minutes, 30 minutes, 60 minutes, 120 minutes, 3 hours, 6 hours, 9 hours, 12 hours, 24 hours, 48 hours and 72 hours after their elective termination of pregnancies. Free fetal DNA was isolated from the plasma and subjected to high throughput sequencing.

RESULTSStatistical analysis of the sequence information showed that the free DNA of fetuses with trisomy 21 or 18 was rapidly cleared after delivery. The average half-life was approximately 1.24 hours within the first 2 hours after delivery. It was then slowly cleared between 6 and 72 hours, with an average half-life of 11.70 hours. No fetal DNA was detectable 72 hours after delivery.

CONCLUSIONFree fetal DNA rapidly decreases after delivery and will completely disappear by 72 hours. Above results may provide a basis for clinical application of the non-invasive detection of chromosomal aneuploidies during prenatal diagnosis.

Adult ; Aneuploidy ; Chromosome Aberrations ; Chromosome Disorders ; diagnosis ; embryology ; genetics ; DNA ; genetics ; Female ; Humans ; Infant, Newborn ; Karyotyping ; Male ; Pregnancy ; Prenatal Diagnosis ; Young Adult

OBJECTIVETo apply single nucleotide polymorphism microarray (SNP array) for the detection of genome-wide copy number variations(CNVs) in fetuses with malformations and women with an adverse reproductive history, and to explore the correlation of rare CNVs with the clinical manifestations.

METHODSAmniotic fluid and umbilical cord blood samples were collected from 314 women with singleton pregnancy. SNP array was performed on samples where chromosomal abnormalities were excluded after G-banding analysis.

RESULTSPathological CNVs were detected in 8.91% (28/314) of all samples, which included 11 duplications, 9 deletions, 4 loss of heterozygosity (LOH), and 4 conjoined deletions and duplications. The sizes of duplications and deletions were between 0.47 Mb and 16.7 Mb, and between 0.16 Mb and 13.3 Mb, respectively. Fifteen CNVs were mapped to the regions of microdeletion or microduplication syndromes or regions associated with clinical manifestations, while the remainder 13 were considered benign or variant of uncertain significance.

CONCLUSIONA proportion of fetuses with malformations and women with an adverse reproductive history may be attributed to CNVs, half of which are mapped with to the regions of well known syndromes. SNP array may facilitate discovery of new syndromes and provide a basis for genetic counseling and prenatal diagnosis.

Adult ; Chromosome Aberrations ; Chromosome Disorders ; diagnosis ; embryology ; genetics ; DNA Copy Number Variations ; Female ; Fetal Diseases ; diagnosis ; genetics ; Humans ; Infant ; Infant, Newborn ; Male ; Polymorphism, Single Nucleotide ; Pregnancy ; Pregnancy Complications ; diagnosis ; genetics ; Prenatal Diagnosis ; Reproductive History ; Young Adult

OBJECTIVETo analyze the correlation between atypical neurofibromatosis type 1(NF1) microdeletion and fetal phenotype.

METHODSFetal blood sampling was carried out for a woman bearing a fetus with talipes equinovarus. G-banded karyotyping and single nucleotide polymorphism array (SNP-array) were performed on the fetal blood sample. Fluorescence in situ hybridization (FISH) was used to confirm the result of SNP array analysis. FISH assay was also carried out on peripheral blood specimens from the parents to ascertain the origin of mutation.

RESULTSThe karyotype of fetus was found to be 46, XY by G-banding analysis. However, a 3.132 Mb microdeletion was detected in chromosome region 17q11.2 by SNP array, which overlaped with the region of NF1 microdeletion syndrome. Analyzing of the specimens from the fetus and its parents with FISH has confirmed it to be a de novo deletion.

CONCLUSIONTalipes equinovarus may be an abnormal sonographic feature of fetus with atypical NF1 microdeletion which can be accurately diagnosed with SNP array.

Adult ; Chromosome Banding ; Chromosome Deletion ; Chromosomes, Human, Pair 17 ; genetics ; Craniofacial Abnormalities ; diagnosis ; embryology ; genetics ; Female ; Gene Deletion ; Humans ; Intellectual Disability ; diagnosis ; embryology ; genetics ; Karyotyping ; Learning Disorders ; diagnosis ; genetics ; Male ; Neurofibromatoses ; diagnosis ; embryology ; genetics ; Neurofibromatosis 1 ; diagnosis ; embryology ; genetics ; Pregnancy ; Prenatal Diagnosis

OBJECTIVETo investigate the prenatal application of single nucleotide polymorphism array (SNP array) in the identification of 5p deletion syndrome with partial trisomy 11q.

METHODSG-banded karyotyping and SNP array were performed using amniocytes on a fetus with multiple malformations for the identification of chromosome abnormality. Furthermore, karyotyping was carried out on the parental peripheral blood specimens to ascertain the origin of chromosome abnormalities and then fluorescence in situ hybridization (FISH) was also utilized to confirm the results.

RESULTSKaryotype of amniocyte showed 46, XY, der(5) (?::p15 → qter). SNP array revealed a 13.907 Mb deletion at 5p15.33p15.2 (chr5: 113576-14020561), overlapping the region of 5p deletion syndrome, and a 18.254 Mb duplication at 11q23.3 q25 (chr11: 116684627-134938470), overlapping no known syndrome. Karyotype of the parents showed a normal 46,XX in mother and 46,XY,t(5;11)(p15;q23) in father. Three-color metaphase FISH analysis on paternal peripheral blood specimens also confirmed the paternal karyotyping result.

CONCLUSIONSNP array could uncover 5p deletion syndrome with partial trisomy 11q unidentified by G-banded karyotyping and accurately locate the genomic breakpoints, facilitating the mapping of pathogenic critical regions and the identification of candidate genes, also accumulating research data for genotype-phenotype study.

Adult ; Chromosome Banding ; Chromosome Deletion ; Chromosome Disorders ; diagnosis ; embryology ; genetics ; Chromosomes, Human, Pair 11 ; genetics ; Chromosomes, Human, Pair 5 ; genetics ; Female ; Humans ; In Situ Hybridization, Fluorescence ; Karyotyping ; Male ; Oligonucleotide Array Sequence Analysis ; methods ; Polymorphism, Single Nucleotide ; Pregnancy ; Prenatal Diagnosis ; methods ; Trisomy ; diagnosis ; genetics

OBJECTIVETo explore the origin of a supernumerary small marker chromosome (sSMC) in a fetus, and to assess the feasibility of single nucleotide polymorphism array (SNP-array) for prenatal diagnosis.

METHODSThe fetal sample was subjected to karyotyping analysis. The identified sSMC was subjected to genome-wide scan using a SNP microarray chip. The results were validated with fluorescence in situ hybridization (FISH).

RESULTSThe karyotype of the fetus was determined as 47,XX,+mar, which was verified by SNP microarray chip analysis as a 34.6 Mb duplication in 12p13.33p11.1. FISH analysis confirmed that the sSMC has originated from chromosome 12p.

CONCLUSIONThe karyotype of the fetus was determined as 47,XX,+i(12)(p10). Tetrasomy 12p is reported to be a marker for Pallister-Killian syndrome, which may result in multi-system anomalies. SNP-array analysis can simultaneously detect microdeletions and microduplications, which may be used for prenatal diagnosis of suspected cases.

Adult ; Chromosome Aberrations ; Chromosome Banding ; Chromosome Disorders ; diagnostic imaging ; embryology ; genetics ; Chromosomes, Human, Pair 12 ; genetics ; Female ; Fetus ; abnormalities ; diagnostic imaging ; metabolism ; Genome-Wide Association Study ; methods ; Humans ; In Situ Hybridization, Fluorescence ; Karyotype ; Karyotyping ; Oligonucleotide Array Sequence Analysis ; methods ; Polymorphism, Single Nucleotide ; Pregnancy ; Ultrasonography, Prenatal ; methods

OBJECTIVETo conduct genetic testing and prenatal diagnosis for a pregnant women with growth retardation, severe mental retardation, and a history of adverse pregnancies.

METHODSG-banded chromosome analysis, fluorescence in situ hybridization (FISH), and whole genome DNA microarray were used to analyze the patient and her fetus.

RESULTSThe women was found to be a chimera containing two cell lines with 47 and 46 chromosomes, respectively. Both have involved deletion of 18q21.2q23. FISH analysis suggested that the cell line containing 47 chromosomes has harbored a chromosome marker derived from chromosome 15. The marker has contained chromosome 15p involving the SNRPN locus and part of 15q, which gave rise to a karyotype of 47,XX,del18q21.3,+ish mar D15Z1+ SNRPN+[82]/46,XX,del18q21.3[18]. Whole genome DNA microarray confirmed that a 3.044 Mb fragment from 15q11.2q12 was duplicated, which involved NIPA1, SNRPN and other 17 OMIM genes. Duplication of this region has been characterized by low mental retardation, autism, developmental delay. Meanwhile, there was a 17.992 Mb deletion at 18q21.33q23, which contained 39 OMIM genes including TNFRSF11A and PHLPP1. This fragment was characterized by mental retardation, developmental delay, short stature, and cleft palate. Whole genome microarray analysis confirmed that there was a 17.9 Mb deletion at 18q21.33q23, which has been implemented with mental retardation, general growth retardation, short stature, and cleft palate. After genetic counseling, the family decided to terminate the pregnancy at 21st week.

CONCLUSIONCombined chromosome karyotyping, FISH, and whole genome DNA microarray can determine the origin of marker chromosomes and facilitate delineation of its correlation with the clinical phenotype.

Abortion, Eugenic ; Adult ; Chromosome Aberrations ; Chromosome Banding ; Chromosomes, Human, Pair 15 ; genetics ; Chromosomes, Human, Pair 18 ; genetics ; Fatal Outcome ; Female ; Fetus ; abnormalities ; metabolism ; Growth Disorders ; embryology ; genetics ; Humans ; In Situ Hybridization, Fluorescence ; Intellectual Disability ; embryology ; genetics ; Karyotype ; Karyotyping ; Prenatal Diagnosis ; methods