[Identification of a novel NF1 mutation in a Chinese family affected with neurofibromatosis type I].

OBJECTIVE: To explore the molecular basis for a Chinese family affected with neurofibromatosis type I. METHODS: Peripheral blood samples were collected from the proband and his parents. Potential mutations of NF1 gene were screened by PCR and Sanger sequencing. Pathogenicity of candidate mutations was analyzed using Polyphen-2 and Provean software. RESULTS: Two mutations of the NF1 gene, including c.702G>A (synonymous mutation) and c.1733T>G (missense mutation), were discovered in the proband. Neither mutation was found in his parents and 50 healthy controls. Bioinformatics analysis indicated that the c.1733T>G mutation (p.Leu578Arg) was probably damaging. The affected codon L578 is highly conserved across various species. CONCLUSION: The c.1733T>C mutation of the NF1 gene probably underlies the neurofibromatosis type I in this family.

Submicroscopic chromosomal imbalances contribute to early abortion.

BACKGROUND: Chromosomal abnormalities are one of the genetic mechanisms associated with abortion. However, the roles of submicroscopic chromosomal imbalances in early abortion are still unclear. This study aims to find out whether submicroscopic chromosomal imbalances contribute to early abortion. METHODS: A total of 78 chorionic villus specimens from early spontaneous abortion patients with no obvious abnormality are collected after miccroassay analysis (the case group). At the same time, 60 chorionic villus specimens from induced abortion patients with no obvious abnormality are selected as the control group. The submicroscopic structures of chromosomes from two groups are analyzed using an array-based comparative genomic hybridization (aCGH). RESULTS: In the case group, 15 specimens show submicroscopic chromosomal abnormalities including 14 micro-deletion/micro-duplication in chromosomes 2, 4, 5, 6, 7, 8, 9, 12, 15, 16, 18, and 22, and 1 uniparental disomy (UPD) in chromosome 19. Moreover, no pathogenic copy number variations are found in the control group. The results between these two groups exhibit significantly statistical difference. CONCLUSION: Submicroscopic chromosomal imbalances may be one of the main reasons for early abortion.

[A novel mutation in the ETFDH gene of an infant with multiple acyl-CoA dehydrogenase deficiency].

This article reports the results of tandem mass spectrometry and the mutation features of the ETFDH gene for an infant with multiple acyl-CoA dehydrogenase deficiency. The results of tandem mass spectrometry showed that C14 : 1, C8, C6, C10, and C12 increased. Exon sequencing was performed on this infant and his parents and revealed double heterozygous mutations in the ETFDH gene of the infant: c.992A>T and c.1450T>C. The former was inherited from his mother, and the latter was inherited from his father. c.1450T>C was shown to be the pathogenic mutation in the HGMD database. PolyPhen2, SIFT, and PROVEAN all predicted that the novel mutation c.992A>T might be pathogenic, and the mutant amino acids were highly conserved across various species. The findings expand the mutation spectrum of the ETFDH gene, and provide molecular evidence for the etiological diagnosis of the patient with multiple acyl-CoA dehydrogenase deficiency as well as for the genetic counseling and prenatal diagnosis in the family.

[Identification of de novo chromosomal structural abnormalities using whole genome sequencing].

OBJECTIVE To assess the value of whole genome sequencing for the identification of de novo structural chromosomal abnormalities. METHODS Whole genome sequencing was utilized to analyze a boy with a peripheral blood karyotype of 46,XY,ins(3)(q21p13p21). The patient manifested with ocular abnormalities including blepharophimosis and ptosis. RESULTS Whole genome sequencing suggested a fragmentation of chromosome 3 (from position 55 473 257 to 78 341 929) has been inserted into between 136 876 730 to 138 643 831, and the breakpoints have occurred in the intergenic region. Meanwhile, there was a deletion between 138 643 831 and 138 694 476. This region contains FOXL2, a pathogenic gene associated with blepharophimosis-ptosis-epicanthus inversus syndrome. CONCLUSION De novo structural chromosomal abnormalities may be caused by novel breakpoints or microdeletion flanking the deletion region. To confirm its pathogenic nature, a mutation needs to be assessed at both genetic and genomic levels, for which whole genome sequencing is a good option.

Detection of complex deletions in chromosomes 13 and 21 in a fetus by noninvasive prenatal testing.

BACKGROUND: To detect complex fetal subchromosomal abnormalities by noninvasive prenatal testing (NIPT). CASE PRESENTATION: After routine prenatal serum screening, the plasma of high-risk pregnant women were tested via NIPT, and the NIPT results were further validated by fetal karyotype analysis and array-based comparative genomic hybridization (aCGH) through amniocentesis. In addition, the chromosome karyotypes of the parents were also analyzed. NIPT results indicated subchromosomal abnormalities in chromosomes 13 and 21; aCGH results showed 22 Mb and 16 Mb deletions in 13 q31.3 - q34 and 21q11.1 - q21.3, respectively; and the fetal karyotype was 45,XX, der(13),-21. The maternal karyotype 46,XX,inv(9)(p12q13),t(13;21)(q31.3;q21.3) was abnormal, while the paternal karyotype showed no obvious abnormality. CONCLUSION: In this study, we successfully detected complex deletions in chromosomes 13 and 21 in a fetus using NIPT, and NIPT can provide effective genetic information for the detection of fetal subchromosomal abnormalities.

[The value of blastocyst culture on preimplantation genetic diagnosis].

OBJECTIVE: To estimate the value of blastocyst culture for preimplantation genetic diagnosis (PGD). METHODS: Day 3 embryos were biopsied and analyzed with fluorescence in situ hybridization (FISH) technique. Embryos with normal FISH results were cultured into blastocysts, and the ones with better morphology scores were transferred. Fourteen embryos with abnormal FISH results were cultured into blastocysts. Part of the cells taken from the blastocysts were amplified by whole genomic amplification (WGA) and assessed by array-based comparative genomic hybridization (array-CGH) analysis. RESULTS: Six blastocysts with normal FISH results were transferred in 5 cycles. Four healthy babies of 3 cycles were delivered. Another one was a singleton pregnancy but with embryo growth arrest, whose villus karyotype was normal. Fourteen embryos with abnormal FISH results were cultured into blastocysts and analyzed by array-CGH. Six blastocysts were normal by array-CGH. CONCLUSION: FISH combined with blastocyst culture may further ensure the accuracy of PGD result. Detection at the blastocyst stage can avoid false positive results and mosaic interferences on Day 3 stage and are therefore more authentic.

Identification of small segmental translocations in patients with repeated implantation failure and recurrent miscarriage using next generation sequencing after in vitro fertilization/intracytoplasmic sperm injection.

BACKGROUND: To develop a novel preimplantation genetic screening (PGS) test using next generation sequencing(NGS) as a alternative to current array comparative genomic hybridization (array CGH) method for detection of small segmental translocations in two patients with repeated implantation failure (RIF) and recurrent miscarriage (RM). Inconsistent results were resolved by validation with fluorescence in situ hybridization (FISH). CASE PRESENTATION: One couple with normal cytogenetic and array CGH result suffered from implantation failure. Later NGS analysis showed 46,XY.ngs[GRCh37/hg19] 9p24.3-9p24.1(10,291-8,680,890×1),13q33.1-13q34(103,046,327-114,785,444×3). The other couple with normal cytogenetic and array CGH result also received NGS analysis. Due to the detected abnormal finding, which was 46,XY.ngs 4q34.3-4q35.2(179,673,982-191,016,503×3),6p25.3-6p22.3 (146,672-17,829,693×1), the couple decided against the corresponding embryo transfer. CONCLUSIONS: The NGS approach is a reliable alternative to array CGH for the discovery of small segmental translocations in patients with RIF and RM.

[Identification of human small supernumerary marker chromosomes and discussion of its research value].

OBJECTIVE: To identify the origin of human small supernumerary marker chromosomes (sSMCs) using fluorescent in situ hybridization (FISH) combined with G-banding karyotype analysis, and to discuss their mechanisms of formation and research value. METHODS: Cep-FISH and SubcenM-FISH were used to analyze sSMCs in 3 patients for whom the result of G-banding was 47,XN,+mar. RESULTS: The FISH result of case 1 was 47,XY,+mar.ish inv dup(22)(q11.1)(D22Z4++,D14/22Z1+, RP11-172D7-). The marker has formed exclusively by heterochromatin. A boy was delivered later with no apparent clinical abnormalities. The FISH result of case 2 was 47,XX,+mar.ish r(10)(p11.2q11.2) (cep10+, RP11-232C13+, RP11-178A10+)[25]/46,XX[10]. The marker has formed by heterochromatin and nearby centromere. A girl was delivered later with no clinical abnormalities. The FISH result of case 3 was 47,XY,+mar.ish inv dup(22)(q11.1)(D22Z4+,D14/22Z1+). The marker has also formed exclusively by euchromatin. Fetal abnormalities were detected by type B ultrasonography, but were not necessarily related with the marker. CONCLUSION: The diversity of sSMCs has posed a great challenge for prenatal diagnosis. Identification of sSMCs will require combined karyotype analysis and FISH or other molecular techniques such as microarray based comparative genomic hybridization or sequencing. For its specific structure, the sSMCs may also provide a valuable tool for gene mapping, heterochromatin research and gene therapy.

Characterization of three small supernumerary marker chromosomes (sSMC) in humans.

In the present study, three prenatally detected small supernumerary marker chromosomes (sSMC) were identified by banding cytogenetics and characterized in detail by molecular cytogenetics. In one case an sSMC(10) leading to a pericentric partial trisomy and in two cases heterochromatic sSMC derived from chromosome 22 were characterized. Outcomes were reportedly normal for two of the three cases for whom this information was known.

Phenotypic and genotypic analysis of biologically cloned human immunodeficiency virus type 1 isolates from patients treated with zidovudine and lamivudine.

Mutations at reverse transcriptase codons 44, 118, 207, and 208 were significantly correlated with reduced zidovudine susceptibility in biologically cloned human immunodeficiency virus type 1 (HIV-1) isolates. Sequences from the Stanford HIV RT and Protease Sequence Database showed that these mutations were more common in HIV-1 isolates from patients treated with zidovudine and lamivudine than in patients not treated with these drugs.