The Setup and Application of Reference Material in Sequencing-Based Noninvasive Prenatal Testing.

INTRODUCTION: The sequencing-based noninvasive prenatal testing (NIPT) has been successfully integrated into clinical practice and facilitated the early detection of fetal chromosomal anomalies. However, a comprehensive reference material to evaluate and quality control NIPT services from different NIPT providers remains unavailable. METHODS: In this study, we established a set of NIPT reference material consisting of 192 simulated samples. Most of the potential factors influencing the accuracy of NIPT, such as fetal fraction, mosaicism, and interfering substances, were included in the reference material. We compared the performance of chromosomal abnormalities detection on 3 widely used sequencers (NextSeq 500, BGISEQ-500, and Ion Proton) based on the reference material. RESULTS: All 3 sequencers provided highly accurate and reliable results to samples with ≥3.5% fetal fractions and high percentage of mosaicism. CONCLUSIONS: The established reference material can serve as a universal standard quality control for the current and new-coming NIPT providers based on various sequencers.

[Identification of a cryptic 1p36.3 microdeletion in a patient with Prader-Willi-like syndrome features].

OBJECTIVE: To determine the karyotype of a patient with Prader-Willi-like syndrome features. METHODS: Chromosomal high resolution banding was carried out to analyze the karyotype of the patient, and methylation-specific PCR was used to analyze the imprinting region of chromosome 15. Subtelomeric region was screened by multiplex ligation-dependent probe amplification (MLPA), and fluorescent in situ hybridization (FISH) and real-time quantitative PCR were further performed to identify the deleted region. RESULTS: No abnormality was discovered by high resolution karyotype analysis and methylation-specific PCR studies. MLPA analysis showed that the patient had a deletion of 1p subtelomeric area, which was confirmed by FISH analysis. The deleted region was shown within a 4.2 Mb in the distal 1p by 3 BAC FISH probes of 1p36 combined with real-time PCR technique. Family pedigree investigation showed the chromosome abnormality was de novo. Therefore, partial monosomy 1p36 was likely responsible for the mental retardation of the patient. CONCLUSION: Molecular cytogenetic techniques should be performed to those patients with Prader-Willi-like syndrome features, to determine their karyotypes.

[Chromosome copy analysis by single-cell comparative genomic hybridization technique based on primer extension preamplification and degenerate oligonucleotide primed-PCR].

OBJECTIVE: To establish a single-cell whole genome amplification (WGA) technique, in combination with comparative genomic hybridization (CGH), for analyzing chromosomal copy number changes, and to explore its clinical application in preimplantation genetic diagnosis (PGD). METHODS: Twelve single-cell samples with known karyotypes, including 5 chorionic villus samples, 4 human embryonic stem cell (hESC) samples and 3 peripheral lymphocyte samples, and 4 single blastomere samples carrying chromosomal abnormalities detected by PGD, were collected for whole genome amplification by combining primer extension preamplification (PEP) with degenerate oligonucleotide primed-PCR (DOP-PCR) amplification. The amplified products labeled by red fluorescence were mixed with control DNA labeled by green fluorescence, and then the mixture was analyzed by CGH. As a comparison, 10 single cell samples were amplified by DOP-PCR only and then CGH analysis was performed. RESULTS: The amplification using PEP-DOP-PCR was more stable than traditional DOP-PCR. The products of PEP-DOP-PCR range from 100 bp to 1000 bp, with the mean size being about 400 bp. The CGH results were consistent with analyses by other methods. However, only 6 out of 10 single cell samples were successfully amplified by DOP-PCR, and CGH analysis showed a high background and 2 samples showed inconsistent results from other methods. CONCLUSION: PEP-DOP-PCR can effectively amplify the whole genome DNA of single cell. Combined with CGH, this WGA method can successfully detect single-cell chromosomal copy number changes, while DOP-PCR was easy to fail to amplify and amplify inhomogeneously, and CGH analysis using this PCR product usually showed high background. These results suggest that PEP-DOP-CGH is a promising method for preimplantation genetic diagnosis.

Crypt Y chromosome fragment resulting from an X;Y translocation in a patient with premature ovarian failure.

OBJECTIVE: To identify a cryptic Y chromosome fragment that resulted from a X;Y translocation in a patient with premature ovarian failure (POF) and analyze the karyotype-phenotype correlation. DESIGN: Case report. SETTING: A university-based reproductive medicine center. PATIENT(S): A 33-year-old woman with POF. INTERVENTION(S): Karyotyping analysis, comparative genomic hybridization, fluorescence in situ hybridization, and polymerase chain reaction (PCR) analysis for the patient. MAIN OUTCOME MEASURE(S): Karyotype determination of the patient. RESULT(S): The patient was suspected to carry an abnormal X chromosome by traditional cytogenetic analysis. A Y chromosome hybridization signal was found in the patient's genome by comparative genomic hybridization analysis. The fluorescence in situ hybridization result showed that the Y chromosome material resulted from a translocation between Xq and Yq. Using the specific sequence-tagged sites, the breakpoints on the X and Y chromosomes were located at Xq26.3 and Yq11.223, respectively. Combined with chromosome G banding and C banding, the karyotype of the patient was determined as 46,X,der(X)t(X;Y) (q26.3;q11.223). CONCLUSION(S): The advanced molecular cytogenetic techniques are helpful to detect cryptic chromosome aberrancies in patients with POF. This rare case supports that Xq26-q28 is the critical region of POF, and is helpful to analyze the risk of gonadoblastoma in patients with POF with Y chromosomal material.

[Delineating a supernumerary marker chromosome by combining several cytogenetic and molecular cytogenetic techniques].

OBJECTIVE: To characterize a supernumerary marker chromosome (SMC) by comparative genomic hybridization (CGH), fluorescence in situ hybridization (FISH) and traditional cytogenetic techniques, and to explore the clinical application of these techniques in delineating de novo marker chromosomes. METHODS: A mental retardation patient received chromosome test by ordinary G banding. CGH and FISH techniques were used to analyze the origin of the de novo SMC, and N banding technique and C banding techniques were used to analyze the SMC structure. The phenotypic effects of the SMC were analyzed after the karyotype was determined. RESULTS: By G banding technique, the patient was showed to have a mosaic karyotype with SMC: mos.47, XX, +mar [31]/48, XX, +2mar[29]. CGH analysis showed a gain of 15q11 --> q14, and the result was confirmed by FISH with chromosome 15 painting probe. The further FISH analysis showed the SMC had two signals with UBE3A probe for detecting Prader-willi syndrome/Angelman syndrome (PWS/AS). N banding and C banding analysis showed the SMC had a double satellite and double centromere, respectively. Combined with the above results, the karyotype of the patient was: mos.47, XX, +der (15) (pter --> q14::q14 --> pter) [31]/48, XX, +2der (15) (pter --> q14::q14 --> pter) [29]. ish der(15)(WCP15+, UBE3A++, PML-). CONCLUSION: CGH is a valuable method to detect imbalanced chromosomal rearrangement. Combined with FISH and the traditional cytogenetic technique, it provides a valuable technique platform for characterizing the structure of the de novo SMC, and a basis for exploring the relation between karyotype and phenotype, prognosis and recurrent risk.

[Identification and characterization of marker chromosome in Turner syndrome].

OBJECTIVE: To analyze the karyotypes of 11 cases of Turner syndrome with marker chromosome, and study the phenotypic effects resulting from the abnormal karyotype. METHODS: Eleven Turner syndrome patients had a mosaic karyotype and carried a marker chromosome, and 6 marker chromosomes were ring chromosomes. Their karyotypes were showed as mos. 45, X/46, X, + mar or mos. 45, X/46, X, + r. Fluorescence in situ hybridization (FISH) technique with X/Y centromere probes was performed to determine the origin of the marker chromosome. Reverse chromosome painting technique was used to identify the breakpoints of two largest markers. Phenotype effects with different chromosome breakpoints were compared. RESULTS: All the 11 marker chromosomes were ring X chromosomes. The breakpoints of the r(X) were involved in Xp22, Xq22, Xq24 and Xq26, etc. CONCLUSIONS: The marker chromosomes in Turner syndrome mainly originate from X chromosome and form ring chromosome X. Each r(X) in our patients was mosaic, indicating it was originated from mitosis error during early embryo development. To analyze the origin of the marker chromosome and the breakpoint of r(X) will provide guidance for the therapy and prognosis of the Turner syndrome patient.