Berry Genomics C. Ltd

Berry, China

Berry Genomics C. Ltd

Berry, China
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Wang Y.,Fudan University | Wang Y.,Shanghai JiaoTong University | Zhu J.,Anhui Medical University | Chen Y.,Shanghai JiaoTong University | And 9 more authors.
Prenatal Diagnosis | Year: 2013

What's already known about this topic? Confined placental mosaicism (CPM) is a known biological phenomenon that can lead to false positive non-invasive prenatal test results. The small number of false negative non-invasive prenatal test results reported to date are believed to be because of a low fetal DNA fraction in maternal plasma and/or placental mosaicism What does this study add? The degree and compartmentalization of placental mosaicism can potentially reduce the effective output of fetal DNA into the maternal circulation to steady state levels below the detection limit of non-invasive prenatal testing, leading to a false negative result © 2013 John Wiley & Sons, Ltd.


Li N.,PLA Fourth Military Medical University | Li N.,Affiliated Hospital of Academy of Military Medical science | Wang L.,Chinese PLA General Hospital | Wang H.,Chinese PLA General Hospital | And 7 more authors.
Journal of Genetics and Genomics | Year: 2015

Reliable and accurate pre-implantation genetic diagnosis (PGD) of patient's embryos by next-generation sequencing (NGS) is dependent on efficient whole genome amplification (WGA) of a representative biopsy sample. However, the performance of the current state of the art WGA methods has not been evaluated for sequencing. Using low template DNA (15pg) and single cells, we showed that the two PCR-based WGA systems SurePlex and MALBAC are superior to the REPLI-g WGA multiple displacement amplification (MDA) system in terms of consistent and reproducible genome coverage and sequence bias across the 24 chromosomes, allowing better normalization of test to reference sequencing data. When copy number variation sequencing (CNV-Seq) was applied to single cell WGA products derived by either SurePlex or MALBAC amplification, we showed that known disease CNVs in the range of 3-15Mb could be reliably and accurately detected at the correct genomic positions. These findings indicate that our CNV-Seq pipeline incorporating either SurePlex or MALBAC as the key initial WGA step is a powerful methodology for clinical PGD to identify euploid embryos in a patient's cohort for uterine transplantation. © 2015 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China.


Song Y.,Peking Union Medical College | Zhou X.,Peking Union Medical College | Huang S.,Peking Union Medical College | Li X.,Peking Union Medical College | And 8 more authors.
Clinica Chimica Acta | Year: 2016

Background: Calculation of the fetal DNA fraction (FF) is important for reliable and accurate noninvasive prenatal testing (NIPT) for fetal genetic abnormalities. The aim of the study was to develop and validate a novel method for FF determination. Methods: FF was calculated using the chromosome Y (ChrY) sequence read assay and by circulating single molecule amplification and re-sequencing technology of 76 autosomal SNPs. Results: By Pearson correlation for FF (4.73-22.11%) in 33 male pregnancy samples, the R2 co-efficient for the 76-SNP versus the ChrY assay was 0.9572 (p < 0.001). In addition, the co-efficient of variation (CV) of FF measurement by the 76-SNP assay was low (0.15-0.35). As a control, the FF measurement for four non-pregnant plasma samples was virtually zero. In prospective longitudinal studies of 14 women with normal pregnancies, FF generally increased with gestational age. However, in eight women (71%) there was a significant decrease in FF between the first trimester (11-13 weeks) and the second trimester (15-19 weeks), and this was attributable to significant maternal weight gain. Conclusions: The novel 76-SNP cSMART assay has the precision to accurately measure FF in all pregnancies at a detection threshold of 5%. Based on FF trends in individual pregnancies, our results suggest that the end of the first trimester may be a more optimal window for performing NIPT. © 2016 Elsevier B.V.


PubMed | Berry Genomics C. Ltd and Peking Union Medical College
Type: | Journal: Clinica chimica acta; international journal of clinical chemistry | Year: 2016

Calculation of the fetal DNA fraction (FF) is important for reliable and accurate noninvasive prenatal testing (NIPT) for fetal genetic abnormalities. The aim of the study was to develop and validate a novel method for FF determination.FF was calculated using the chromosome Y (ChrY) sequence read assay and by circulating single molecule amplification and re-sequencing technology of 76 autosomal SNPs.By Pearson correlation for FF (4.73-22.11%) in 33 male pregnancy samples, the R(2) co-efficient for the 76-SNP versus the ChrY assay was 0.9572 (p<0.001). In addition, the co-efficient of variation (CV) of FF measurement by the 76-SNP assay was low (0.15-0.35). As a control, the FF measurement for four non-pregnant plasma samples was virtually zero. In prospective longitudinal studies of 14 women with normal pregnancies, FF generally increased with gestational age. However, in eight women (71%) there was a significant decrease in FF between the first trimester (11-13 weeks) and the second trimester (15-19 weeks), and this was attributable to significant maternal weight gain.The novel 76-SNP cSMART assay has the precision to accurately measure FF in all pregnancies at a detection threshold of 5%. Based on FF trends in individual pregnancies, our results suggest that the end of the first trimester may be a more optimal window for performing NIPT.


Fan J.,Chinese PLA General Hospital | Wang L.,Chinese PLA General Hospital | Wang H.,Chinese PLA General Hospital | Ma M.,Chinese PLA General Hospital | And 6 more authors.
Reproductive BioMedicine Online | Year: 2015

Abstract Next-generation sequencing is emerging as a reliable and accurate technology for pre-implantation genetic diagnosis (PGD) of aneuploidies and translocations. The aim of this study was to extend the clinical utility of copy number variation sequencing (CNV-Seq) to the detection of small pathogenic copy number variations (CNVs) associated with chromosome disease syndromes. In preliminary validation studies, CNV-Seq was highly sensitive and specific for detecting small CNV in whole-genome amplification products from three replicates of one and five cell samples, with a resolution in the order of 1-2 Mb. Importantly, the chromosome positions of all CNV were correctly mapped with copy numbers similar to those measured in matching genomic DNA samples. In seven clinical PGD cycles where results were obtained for 34 of 35 blastocysts, CNV-Seq identified 18 blastocysts with aneuploidies, one with an aneuploidy and a 4.98 Mb 5q35.2-qter deletion associated with Sotos syndrome, one with a 6.66 Mb 7p22.1-pter deletion associated with 7p terminal deletion syndrome and 14 with no detectable abnormalities that were suitable for transfer. On the basis of these findings, CNV-Seq displays the hallmarks of a comprehensive PGD technology for detection of aneuploidies and CNVs that are known to affect the development and health of patient's embryos. © 2015 Reproductive Healthcare Ltd.


Chen C.,Wenzhou Medical College | Cram D.S.,Berry Genomics C. Ltd | Xie F.,Wenzhou Medical College | Wang P.,Wenzhou Medical College | And 8 more authors.
Reproductive BioMedicine Online | Year: 2014

This study investigated a pregnancy where the fetus was diagnosed with monosomy 18p by invasive amniocentesis and karyotyping. Additional noninvasive prenatal diagnosis, which detects fetal chromosome abnormalities in the circulating cell-free plasma DNA originating from the placenta revealed a related 18p monosomy/18q trisomy, suggesting confined placental mosaicism. Based on recent observations of chromosomal instability in the early preimplantation embryo, this study speculates on the possible embryonic origin(s) of these related but discordant chromosome 18 aneuploidies in the placental and fetal tissues. The findings highlight the potential for both false-positive and -negative noninvasive prenatal diagnosis results in pregnancies where there is either confined placental mosaicism or placental mosaicism. The study investigated a pregnancy involving a fetus with a chromosome disease syndrome called monosomy 18p where part of the short arm of chromosome 18 was missing in the fetal tissues. Using non-invasive prenatal diagnosis which detects fetal chromosome abnormalities in the circulating cell free plasma DNA originating from the placenta, we also detected monosomy 18p as well a related chromosome 18 abnormality involving duplication of the long arm of chromosome 18. This suggested confined placental mosaicism where the constitution of the chromosomes are different between fetal and placental tissues. We speculated that these related chromosome 18 abnormalities arose during preimplantation embryo development, leading to the formation of different chromosome abnormalities observed in the placental and fetal tissues of this pregnancy. Our findings highlight the potential for both false positive and negative non-invasive prenatal diagnosis test results in pregnancies where there is confined placental mosaicism. © 2014, Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.


Mao J.,Nanjing Medical University | Wang T.,Nanjing Medical University | Wang B.-J.,Nanjing Medical University | Liu Y.-H.,Nanjing Medical University | And 4 more authors.
Clinica Chimica Acta | Year: 2014

Background: Non-invasive prenatal testing (NIPT) by massively parallel sequencing is a useful clinical test for the detection of common fetal aneuploidies. While the accuracy of aneuploidy detection can approach 100%, results discordant with the fetus are occasionally reported. In this study we investigated the basis of a discordant T21 positive and T18 negative NIPT result associated with a T18 fetus confirmed by karyotyping. Methods: Massively parallel sequencing was used to detect fetal DNA in maternal circulating plasma. The parental origin and nature of the fetal and placental aneuploidies were investigated by quantitative fluorescent PCR of short tandem repeat (STR) sequences and by copy number variation (CNV) sequencing. Results: There was no evidence of T21 maternal mosaicism, T21 microchimerism or a vanishing twin to explain the discordant NIPT result. However, examination of multiple placental biopsies showed both T21 and T18 mosaicism, including one confined region with a significantly higher proportion of T21 cells. Based on fetal DNA fractions and average mosaicism levels, the effective T21 and T18 fetal DNA fractions should have been sufficient for the detection of both trisomies. Conclusions: In this pregnancy, we speculate that confined placental region(s) with higher proportions of T21 cells were preferentially releasing fetal DNAs into the maternal circulation. This study highlights placental mosaicism as a significant risk factor for discordant NIPT results. © 2014 Elsevier B.V.

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