1.Comparison of SNP-array and next generation sequencing in preimplantation genetic testing
Hong ZHOU ; Yueyun LAN ; Jinhui SHU ; Caizhu WANG ; Xin ZHAO ; Lifang LIANG ; Sheng HE ; Qingming QIU ; Peng HUANG
Chinese Journal of Reproduction and Contraception 2023;43(10):1018-1025
Objective:To evaluate the detection ability and efficiency of single nucleotide polymorphisms array (SNP-array) and next generation sequencing (NGS) in preimplantation genetic testing (PGT).Methods:Totally 188 couples who carried pathogenic gene mutation and requested preimplantation genetic testing for monogenic (PGT-M) treatment were retrospectively analyzed in the Reproductive Center of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region during January 2020 and August 2022. After ovulation induction, insemination was conducted by intracytoplasmic sperm injection (ICSI) and cultured in vitro, 995 blastocysts were harvested and biopsied. After whole genome amplification (WGA) of the genetic material from embryonic cell samples, their carrying status of mutations and chromosome copy number variations (CNVs) were analyzed by SNP-array or NGS, respectively, and along with mutation direct detection by Sanger sequencing or Gap-PCR. The relationship between female age and the number of blastocysts was analyzed, as well as the proportion of embryos carrying mutations and pathogenic CNVs. The detection success rate and accuracy of different molecular diagnostic techniques used in PGT were compared. Amniocentesis prenatal diagnosis was performed in the second trimester after successful intrauterine transfer of embryos. Results:1) A total of 924 embryo samples were successfully performed genetic testing, with a total success rate of 92.9%, and 389 embryos (42.1%) can be transferred according to these results. 2) In detecting deletional α-thalassemia, the success rate of Gap-PCR [84.9% (465/548)] was lower than that of SNP-array [98.7% (81/82)] and NGS [92.5% (431/466)]. However, the success rate of direct mutation detection by Sanger sequencing [98.5% (440/447)] was not significantly different from that by SNP-array [95.6% (110/115)] and NGS [96.1% (319/332)]. There were 38 embryo samples with direct mutation detection results inconsistent with those based on SNP haplotyping. In addition, 4 embryo samples failed SNP haplotyping due to chromosomal recombination. 3) Compared with NGS, SNP-array had a lower success rate [83.7% (165/197)] in detecting CNVs, but it could find out more types of chromosomal abnormalities. 4) A total of 152 embryo transfers were performed, 107 patients got clinical pregnancies, 69 patients completed amniocentesis prenatal diagnosis, and 42 healthy infants were delivered.Conclusion:In considering the detection efficiency, SNP-array is suitable for analyzing embryos which carry multiple pathogenic genes, rare monogenic or deletion mutations, whereas NGS is suitable for detecting common types of mutations. Meanwhile, using Sanger sequencing and Gap-PCR to directly detect the mutations can improve the success rate and accuracy of PGT. Our findings would provide a basis for PGT technicians to select appropriate detection platforms based on the type of mutations and the situation of patients.
2.Comparison of SNP-array and next generation sequencing in preimplantation genetic testing
Hong ZHOU ; Yueyun LAN ; Jinhui SHU ; Caizhu WANG ; Xin ZHAO ; Lifang LIANG ; Sheng HE ; Qingming QIU ; Peng HUANG
Chinese Journal of Reproduction and Contraception 2023;43(10):1018-1025
Objective:To evaluate the detection ability and efficiency of single nucleotide polymorphisms array (SNP-array) and next generation sequencing (NGS) in preimplantation genetic testing (PGT).Methods:Totally 188 couples who carried pathogenic gene mutation and requested preimplantation genetic testing for monogenic (PGT-M) treatment were retrospectively analyzed in the Reproductive Center of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region during January 2020 and August 2022. After ovulation induction, insemination was conducted by intracytoplasmic sperm injection (ICSI) and cultured in vitro, 995 blastocysts were harvested and biopsied. After whole genome amplification (WGA) of the genetic material from embryonic cell samples, their carrying status of mutations and chromosome copy number variations (CNVs) were analyzed by SNP-array or NGS, respectively, and along with mutation direct detection by Sanger sequencing or Gap-PCR. The relationship between female age and the number of blastocysts was analyzed, as well as the proportion of embryos carrying mutations and pathogenic CNVs. The detection success rate and accuracy of different molecular diagnostic techniques used in PGT were compared. Amniocentesis prenatal diagnosis was performed in the second trimester after successful intrauterine transfer of embryos. Results:1) A total of 924 embryo samples were successfully performed genetic testing, with a total success rate of 92.9%, and 389 embryos (42.1%) can be transferred according to these results. 2) In detecting deletional α-thalassemia, the success rate of Gap-PCR [84.9% (465/548)] was lower than that of SNP-array [98.7% (81/82)] and NGS [92.5% (431/466)]. However, the success rate of direct mutation detection by Sanger sequencing [98.5% (440/447)] was not significantly different from that by SNP-array [95.6% (110/115)] and NGS [96.1% (319/332)]. There were 38 embryo samples with direct mutation detection results inconsistent with those based on SNP haplotyping. In addition, 4 embryo samples failed SNP haplotyping due to chromosomal recombination. 3) Compared with NGS, SNP-array had a lower success rate [83.7% (165/197)] in detecting CNVs, but it could find out more types of chromosomal abnormalities. 4) A total of 152 embryo transfers were performed, 107 patients got clinical pregnancies, 69 patients completed amniocentesis prenatal diagnosis, and 42 healthy infants were delivered.Conclusion:In considering the detection efficiency, SNP-array is suitable for analyzing embryos which carry multiple pathogenic genes, rare monogenic or deletion mutations, whereas NGS is suitable for detecting common types of mutations. Meanwhile, using Sanger sequencing and Gap-PCR to directly detect the mutations can improve the success rate and accuracy of PGT. Our findings would provide a basis for PGT technicians to select appropriate detection platforms based on the type of mutations and the situation of patients.
3.Influence of effects of transarterial chemoembolization before liver transplantation on the prognosis of hepatocellular carcinoma
Xiongwei ZHU ; Ziqiang LI ; Yan TIAN ; Bo YOU ; Yang YANG ; Bin LU ; Zehao WU ; Qing ZHANG ; Qingming SHU
Chinese Journal of Digestive Surgery 2022;21(2):256-264
Objective:To investigate the influence of effects of transarterial chemoembo-lization (TACE) before liver transplantation on the prognosis of hepatocellular carcinoma.Methods:The retrospective cohort study was conducted. The clinicopathological data of 311 hepatocellular carcinoma patients undergoing TACE before liver transplantation who were admitted to the Third Medical Center of Chinese PLA General Hospital from January 2005 to December 2012 were collec-ted. There were 276 males and 35 females, aged from 47 to 59 years, with a median age of 52 years. All the 311 patients underwent TACE before liver transplantation. Observation indicators: (1) effects of hepatocellular carcinoma patients undergoing TACE and its relationship with clinicopathological factors; (2) follow-up; (3) influencing factors for prognosis of hepatocellular carcinoma patients after liver transplantation. Follow-up was conducted using outpatient examination or telephone interview to detect recurrence and metastasis of tumor and survival and graft loss of patients up to December 2017. The patients were followed up every 2 to 4 weeks within 3 months after liver transplantation, and once every 1 to 3 months thereafter. Measurement data with normal distri-bution were represented as Mean± SD, and comparison between groups was analyzed using the t test. Measurement data with skewed distribution were represented as M(range) or M( Q1, Q3), and comparison between groups was analyzed using the Mann-Whitney U test. Count data were described as absolute numbers or percentages, and comparison between groups was analyzed using the chi-square test. Comparison of ordinal data was analyzed using the nonparametric rank sum test. The COX regression model was used for univariate and multivariate analyses. The Kaplan-Meier method was used to draw survival curves and calculate survival rates, and the Log-rank test was used for survival analysis. Results:(1) Effects of hepatocellular carcinoma patients undergoing TACE and its relationship with clinicopathological factors. Of the 311 patients undergoing TACE, 57 cases had pathologic complete response (pCR) and 254 cases had pathologic partial response (pPR), respectively. Cases with alpha fetoprotein (AFP) <20 μg/L,20?400 μg/L, >400 μg/L, cases with microvascular invasion, cases with tumor number as single nodule, cases with tumor distribution at right lobe of liver, cases with tumor caliber of feeding artery (CFA) >1 mm were 26, 26, 5, 51, 6, 43, 46 in patients with pCR, versus 87, 64, 103, 158, 59, 125, 159 in patients with pPR, showing significant differences in the above indicators ( Z=3.35, χ2=4.54, 15.71, 12.89, 6.79, P<0.05). (2) Follow-up. All the 311 patients were followed up for 47.0 to 59.0 months, with a median follow-up time of 44.6 months. There were 11 cases undergoing tumor recurrence and 11 cases undergoing tumor metastasis in the 57 patients with pCR, and there were 96 cases undergoing tumor recurrence and 66 cases under-going tumor metastasis in the 254 patients with pPR. The 1-, 3-, 5-year tumor recurrence free rates were 98.2%, 91.1%, 80.3% in the 311 patients, respectively. The 1-, 3-, 5-year tumor recurrence free rates were 100.0%, 91.1%, 80.3% in the 57 patients with pCR, versus 82.0%, 68.4%, 59.4% in the 254 patients with pPR, showing significant differences in the above indicators ( χ2=13.47, P<0.05). Cases with graft loss were 11 and 96 in the 57 patients with pCR and the 254 patients with pPR, respectively, showing a significant difference ( χ2=7.06, P<0.05). (3) Influen-cing factors for prognosis of hepatocellular carci-noma patients after liver transplantation. Results of univariate analysis showed that gender, basic diseases as viral hepatitis C, AFP (20?400 μg/L, >400 μg/L), Milan criteria, microvascular invasion, tumor number, tumor distribution, tumor CFA, times of TACE, effects of TACE were related factors influencing prognosis of hepatocellular carcinoma patients after liver transplantation ( hazard ratio=0.49, 3.97, 1.78, 1.84, 2.41, 1.96, 3.00, 1.76, 0.19, 2.01, 3.07, 95% confidence interval as 0.30?0.81, 2.23?7.05, 1.03?3.06, 1.18?2.85, 1.63?3.56, 1.28?3.01, 2.04?4.40, 1.20?2.59, 0.13?0.28, 1.28?3.14, 1.63?5.76, P<0.05). Results of multi-variate analysis showed that AFP >400 μg/L, exceeding Milan criteria, tumor number as multiple nodule,effects of TACE as pPR were independent risk factors influencing prognosis of hepatocellular carcinoma patients after liver transplantation ( hazard ratio=1.59, 2.06, 1.99, 2.05, 95% confidence interval as 1.22?2.07, 1.35?3.13, 1.29?3.07, 1.02?4.10, P<0.05) and tumor CFA >1 mm was an independent protective factor influencing prognosis of hepatocellular carcinoma patients after liver transplantation ( hazard ratio=0.10, 95% confidence interval as 0.05?0.19, P<0.05). Conclusions:The effects of TACE are related to AFP, microvascular invasion, tumor number, tumor distribution and tumor CFA. AFP >400 μg/L, exceeding Milan criteria, tumor number as multiple nodule,effects of TACE as pPR are independent risk factors influencing prognosis of hepatocellular carcinoma patients after liver transplantation and tumor CFA >1 mm is an independent protective factor influencing prognosis of hepatocellular carcinoma patients after liver transplantation.
4.Primary study of real time elastosonography in estimating the characteristic of nodes in resected hepatocirrhosis specimens
Xiuyun REN ; Hui XU ; Qingming SHU ; Xiaomei LI ; Hong NIU
Chinese Journal of Ultrasonography 2010;19(1):29-31
Objective To evaluate the feasibility of real time elastosonography in estimating the characteristic of nodules in resected hepatocirrhosis specimens.Methods Thirty-eight reseeted hepatocirrhosis specimens underwent elastosonography.The nodules that have drawn attention were performed elastosonography through rhythmic pressing and releasing the probe by manual form on the liver.The hepatic strain on the region of interest was shown by chromatic scale.To compare nodules rigidity with surrounding hepatic tissues, hepatocirrhosis nodules were classified into hard nodules, medium rigidity nodules, mixture of hard and soft nodules, and soft nodules.All nodules were confirmed by pathology.Results Forty-four nodules of 38 hepatocirrhosis exemplar received real time elastosonography.Of 44 nodules, hard nodules were 18,of which 12 (66.7%) were hepatoeellular carcinomas, 2 (11.1%) were dysplasia nodules, 4 (22.2%) were regenerative nodules.Medium rigidity nodules were 7,all were regenerative nodules.Mixture of hard and soft nodules were 11, of which 8 (72.7%) were hepatocellular carcinomas, including 4 accompanied necrotic tissue, 1 (9.1%) was dysplasia nodules accompanied necrotic tissue, the other 2 (18.2%) were regenerative nodules accompanied necrotic tissue.And soft nodules were 8, of which 4(50.0%) were necrotic nodules, 1 (12.5%) was dysplasia nodules accompanied canceration, 1 (12.5%) was hepatocellular carcinoma,2(25.0 %) were regenerative nodules.Conclusions Real time elastosonography can effectively evaluate the comparative rigidity on hepatoeirrhosis nodules,and thus may have potential usefulness on estimating the characteristic of hepatocirrhosis nodules.

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