Noninvasive prenatal detection of hemoglobin Bart hydrops fetalis via maternal plasma dispensed with parental haplotyping using the semiconductor sequencing platform.

BACKGROUND: Thalassemia is one of the most common monogenetic diseases in the south of China and Southeast Asia. Hemoglobin Bart's hydrops fetalis syndrome was caused by a homozygous Southeast Asian deletion (-/-) in the HBA gene. Few studies have proved the potential of screen for Bart's hydrops fetalis using fetal cell-free DNA. However, the number of cases is still relatively small. Clinical trials of large samples would be needed. OBJECTIVE: In this study, we aimed to develop a noninvasive method of target-captured sequencing and genotyping by the Bayesian method using cell-free fetal DNA to identify the fetal genotype in pregnant women who are at risk of having hemoglobin Bart hydrops fetalis in a large-scale study. STUDY DESIGN: In total, 192,173 couples from 30 hospitals were enrolled in our study and 878 couples were recruited, among whom both the pregnant women and their husbands were detected to be carriers of Southeast Asian type (-/αα) of α-thalassemia. Prenatal diagnosis was performed by chorionic villus sampling, amniocentesis, or cordocentesis using gap-polymerase chain reaction considered as the golden standard. RESULTS: As a result, we found that the sensitivity and specificity of our noninvasive method were 98.81% and 94.72%, respectively, in the training set as well as 100% and 99.31%, respectively, in the testing set. Moreover, our method could identify all of 885 maternal samples with the Southeast Asian carrier and 36 trisomy samples with 100% of sensitivity in T13, T18, and T21 and 99.89% (1 of 917) and 99.88% (1 of 888) of specificity in T18 and T21, respectively. CONCLUSION: Our method opens the possibility of early screening for maternal genotyping of α-thalassemia, fetal aneuploidies in chromosomes 13/18/21, and hemoglobin Bart hydrops fetalis detection in 1 tube of maternal plasma.

Preimplantation genetic diagnosis and screening (PGD/S) using a semiconductor sequencing platform.

BACKGROUND: Recent advances in semiconductor sequencing platform (SSP) have provided new methods for preimplantation genetic diagnosis/screening (PGD/S). The present study aimed to evaluate the applicability and efficiency of SSP in PGD/S. METHODS: The artificial positive single-cell-like DNAs and normal single-cell samples were chosen to test our semiconductor sequencing platform for preimplantation genetic diagnosis/screening (SSP-PGD/S) method with two widely used whole-genome amplification (WGA) kits. A total of 557 single blastomeres were collected from in vitro fertilization (IVF) couples, and their WGA products were processed and analyzed by our SSP-PGD/S method in comparison with array comparative genomic hybridization (array-CGH). RESULTS: Our SSP-PGD/S method indicated high compatibilities with two commercial WGA kits. For 557 single blastomeres, our method with four million reads in average could detect 24-chromosome aneuploidies as well as microdeletion/microduplication of the size over 4 Mb, providing 100% consistent conclusion with array-CGH method in the classification of whether it was transplantable. CONCLUSIONS: Our studies suggested that SSP-PGD/S represents a valuable alternative to array-CGH and brought PGD/S into a new era of more rapid, accurate, and economic.

[Association of the H770H of PR gene polymorphism with susceptibility to endometriosis].

OBJECTIVE: To investigate the association of PR gene exon 5 region H770H (rs1042839) single nucleotide polymorphism (SNP) with the genetic susceptibility to endometriosis (EM) in southern Han Chinese women. METHODS: Totally 431 EM patients and 499 non-EM women were collected and separated into EM group and control group, that all cases were confirmed by operation and pathology. A case-control study was performed in EM and control groups to evaluate the association of these SNP with the susceptibility to EM by using a fluorescent quantitative PCR-based high resolution melting (HRM) method. RESULTS: The C and T of PR H770H allele frequencies among the EM and control groups were 97.9% (844/862), 2.1% (18/862) and 99.4% (992/998), 0.6% (6/998), respectively. The CC, CT and TT of PR H770H genotype frequencies among the EM and control groups were 95.8% (413/431), 4.2% (18/431), 0 and 98.8% (493/499), 1.2% (6/499), 0, respectively. There were statistical significances in the PR H770H alleles and genotypes distributions between the two groups (χ(2)=7.386, P=0.007; χ(2)=8.135, P=0.004). Carrying allele C reduced the risk of EM (OR=0.986, 95%CI: 0.976-0.996), while carrying allele T enhanced the risk of EM (OR=3.319, 95% CI: 1.323-8.325); carrying genotype CC reduced the risk of EM 0.970 time (OR=0.970, 95% CI: 0.949-0.991), whereas carrying genotype CT enhanced the risk of EM 3.473 times (OR=3.473, 95%CI: 1.391-8.671). CONCLUSION: There is significant association between the polymorphism of PR H770H and genetic susceptibility to EM in southern Han Chinese women.

[Relationship of polymorphisms of AhR -1661G/A with GSTP1 -313A/G and susceptibility to endometriosis].

OBJECTIVE: To investigate the association of polymorphisms of arylhydrocarbon receptor (AhR)-1661G/A with glutathione S-transferase pi (GSTP1) -313A/G and the susceptibility to endometriosis in southern Han Chinese. METHODS: Total of 432 endometriosis patients undergoing laparoscopic or laparotomy surgery matched with 493 patients with fallopian tube ligation, tubal recanalization, laparoscopic hydrotubation, benign ovarian tumor and teratoma surgeries without endometriosis as control group were enrolled in this study. The single nucleotide polymorphism (SNP) of AhR -1661G/A and GSTP1 -313A/G were detected by using a fluorescent quantitative PCR-based high resolution melting (HRM). RESULTS: The numbers of combined genotypes AhR -1661G/A and GSTP1 -313A/G were 120 patients with AG + AA, 64 patients with AG + AG, 8 patients with AG + GG, 109 patients with GG + AA, 84 patients with GG + AG, 4 patients with GG + GG, 31 patients with AA + AA, 10 patients with AA + AG, 1 patient with AA + GG at endometriosis group and 131 patients with AG + AA, 68 patients with AG + AG, 6 patients with AG + GG, 157 patients with GG + AA, 66 patients with GG + AG, 4 patients with GG + GG, 35 patients with AA + AA, 20 patients with AA + AG, 3 patients with AA + GG at endometriosis group. There was no statistically different frequencies of genotypes between endometriosis group and control group (χ(2) = 12.558, P = 0.128). Compared with genotype GG + AA, the risk of endometriosis with genotype GG + AG was increased 1.833 time (95%CI: 1.233 - 2.274). CONCLUSION: The combined genotype GG + AG [from AhR -1661G/A (GG) and GSTP1 -313A/G (AG)] might be related with susceptibility to endometriosis.

[Association of the tumor necrosis factor-alpha -1031T/C and its combination with interleukin-6 -634C/G gene polymorphisms with susceptibility to endometriosis].

OBJECTIVE: To investigate the association of tumor necrosis factor-alpha (TNF-α) gene promoter region -1031T/C and its combination with interleukin-6 (IL-6) gene promoter region -634C/G single nucleotide polymorphisms (SNP) with the genetic susceptibility to endometriosis. METHODS: Total of 432 endometriosis patients and 499 non-endometriosis women who had received an operation due to tubal ligation, tubal recanalization, laparoscopic hydrotubation, ovarian simple cyst and teratoma were collected and separated into endometriosis group and control group, that all cases were confirmed by operation and pathology. A case-control study was performed in endometriosis and control group to evaluate the association of these SNP with the susceptibility to endometriosis by using a fluorescent quantitative PCR-based high resolution melting (HRM) method. RESULTS: (1) TNF-α -1031T/C genotype:the T and C of TNF-α -1031T/C allele frequencies in the endometriosis group and control group were 79.2% (684/864), 20.8% (180/864) and 81.8% (816/998), 18.2% (182/998), respectively. The TT, TC and CC of TNF-α -1031T/C genotype frequencies in the two groups were 63.7% (275/432), 31.0% (134/432), 5.3% (23/432) and 66.5% (332/499), 30.5% (152/499), 3.0% (15/499), respectively. There were no statistical significances in the TNF-α -1031T/C alleles and genotypes distributions between the two groups (P = 0.158, P = 0.186). (2) TNF-α -1031T/C and IL-6 -634C/G conjoint genotypes: to research on the TNF-α -1031T/C and IL-6 -634C/G genotypes for conjoint analysis, the TT+CC, TC+CC, CC+CC, TT+CG, TC+CG, CC+CG, TT+GG, TC+GG and CC+GG combination genotype frequencies in the two groups were 39.4% (170/432), 19.4% (84/432), 4.6% (20/432), 20.6% (89/432), 8.8% (38/432), 0.9% (4/432), 3.5% (15/432), 2.3% (10/432), 0.5% (2/432) and 36.7% (183/499), 17.4% (87/499), 1.4% (7/499), 26.1% (130/499), 10.4% (52/499), 1.2% (6/499), 3.8% (19/499), 2.6% (13/499), 0.4% (2/499), respectively. There were no statistical significances in the combination genotypes distributions between the two groups (P = 0.107). As compared with carriers of TT+CC combination genotype, the endometriosis risk of carriers of CC+CC combination genotype enhanced 3.076 times (95%CI: 1.268 - 7.457, P = 0.009), and the endometriosis risk of carriers of other combination genotypes were no statistical significances (all P > 0.05). CONCLUSIONS: The study demonstrates that there are no significant association between the SNP of TNF-α -1031T/C and genetic susceptibility to endometriosis. However the results indicate that there are significant association between genetic susceptibility to endometriosis and the combination polymorphisms of TNF-α -1031T/C and IL-6 -634C/G.

HTS-PEG: a method for high throughput sequencing of the paired-ends of genomic libraries.

Second generation sequencing has been widely used to sequence whole genomes. Though various paired-end sequencing methods have been developed to construct the long scaffold from contigs derived from shotgun sequencing, the classical paired-end sequencing of the Bacteria Artificial Chromosome (BAC) or fosmid libraries by the Sanger method still plays an important role in genome assembly. However, sequencing libraries with the Sanger method is expensive and time-consuming. Here we report a new strategy to sequence the paired-ends of genomic libraries with parallel pyrosequencing, using a Chinese amphioxus (Branchiostoma belcheri) BAC library as an example. In total, approximately 12,670 non-redundant paired-end sequences were generated. Mapping them to the primary scaffolds of Chinese amphioxus, we obtained 413 ultra-scaffolds from 1,182 primary scaffolds, and the N50 scaffold length was increased approximately 55 kb, which is about a 10% improvement. We provide a universal and cost-effective method for sequencing the ultra-long paired-ends of genomic libraries. This method can be very easily implemented in other second generation sequencing platforms.

[Association of the IL-6 gene 634C/G polymorphism with susceptibility to endometriosis].

OBJECTIVE: To investigate the association of interleukin 6 gene (IL-6) promoter region 634C/G (rs1800796) single nucleotide polymorphism (SNP) with the genetic susceptibility to endometriosis (Ems) in south Han Chinese women. METHODS: A case-control study was performed in 432 Ems patients and 499 control women to evaluate the SNP of IL-6 634C/G by using a fluorescent quantitative PCR-based high resolution melting (HRM) method. RESULTS: There were statistical significances in the IL-6 634C/G alleles, whether or not to carry allele G and genotype distributions between Ems patients and control women (P=0.032, 0.014 and 0.045, respectively). Allele C enhanced the risk of Ems 1.057 times while allele G reduced the risk of Ems 0.835 time. Carrying allele G reduced the risk of Ems 0.822 time, whereas not carrying allele G enhanced the risk of Ems 1.143 times. Compared with genotype CC, the risk of Ems with genotype CG reduced 0.704 time (95% CI: 0.533-0.931). There was no significant difference in whether or not carrying allele G distribution between Ems patients and control women (P=0.729). CONCLUSION: The present study demonstrated significant association between the SNP of IL-6 634C/G and genetic susceptibility to Ems in south Han Chinese women.

[Association of single nucleotide polymorphism in CYP17 and ERα genes with endometriosis risk in southern Chinese women].

OBJECTIVE: To investigate the association of single nucleotide polymorphisms in cytochrome P450 17 (CYP17) and estrogen receptor alpha (ERα ) genes with the risk of endometriosis among southern Chinese women. METHODS: Two SNPs rs743572 (CYP17 gene 34T/C) and rs9322331 (ERα gene -397T/C) were genotyped by high resolution melting curve in 432 endometriosis patients and 499 matched controls. RESULTS: There was no significant difference in the genotype frequencies of the two loci between endometriosis patients and the control subjects (P> 0.05). And there was no significant interaction effect of these two genes on the disease either. CONCLUSION: CYP17 gene and ERα gene may not be genetic risk factors for endometriosis among southern women in China.

[No association of AhR gene 1661G/A and ARNT gene 567G/C polymorphisms with endometriosis in southern Han Chinese women].

OBJECTIVE: To explore the association between the arylhydrocarbon receptor gene (AhR) 1661G/A or arylhydrocarbon nuclear translocatorgene (ARNT) 567G/C polymorphism and endometriosis in southern Han Chinese women. METHODS: The polymorphisms of AhR gene 1661G/Aand ARNT gene 567G/C in 431 cases of endometriosis and 499 healthy women were genotyped by fluorescence quantitative PCR-based high resolution melting. RESULTS: The frequencies of genotypes AA, AG, GG and alleles A and G in controls were 12.0%, 41.9%, 46.1%, 33.0% and 67.0%, respectively, which were not significantly different from those in patients with endometriosis (9.7%, 44.6%, 45.7%, 32.0% and 68.0%, respectively). The genotype frequencies of GG, GC, CC and alleles C and G in controls (15.6 %, 51.7%, 32.7%, 58.5%, 41.5%) were not significantly different from those in patients with endometriosis (13.5%, 47.8%, 38.7%, 62.6%, 37.4%), either. And no interaction of AhR 1661G/A and ARNT 567G/C on endometriosis was found. CONCLUSION: No association between AhR 1661G/A and ARNT 567G/C genetic polymorphisms and endometriosis was found in the southern Han Chinese women in this study.

Differential genome-wide profiling of tandem 3' UTRs among human breast cancer and normal cells by high-throughput sequencing.

Tandem 3' UTRs produced by alternative polyadenylation (APA) play an important role in gene expression by impacting mRNA stability, translation, and translocation in cells. Several studies have investigated APA site switching in various physiological states; nevertheless, they only focused on either the genes with two known APA sites or several candidate genes. Here, we developed a strategy to study APA sites in a genome-wide fashion with second-generation sequencing technology which could not only identify new polyadenylation sites but also analyze the APA site switching of all genes, especially those with more than two APA sites. We used this strategy to explore the profiling of APA sites in two human breast cancer cell lines, MCF7 and MB231, and one cultured mammary epithelial cell line, MCF10A. More than half of the identified polyadenylation sites are not included in human poly(A) databases. While MCF7 showed shortening 3' UTRs, more genes in MB231 switched to distal poly(A) sites. Several gene ontology (GO) terms and pathways were enriched in the list of genes with switched APA sites, including cell cycle, apoptosis, and metabolism. These results suggest a more complex regulation of APA sites in cancer cells than previously thought. In short, our novel unbiased method can be a powerful approach to cost-effectively investigate the complex mechanism of 3' UTR switching in a genome-wide fashion among various physiological processes and diseases.