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Hao Liu, Wang He, Bo Wang, Kewei Xu, Jinli Han, Junjiong Zheng, Jun Ren, Lin Shao, Shiping Bo, Sijia Lu, Tianxin Lin, Jian Huang
BACKGROUND: The gold standard for bladder cancer detection is cystoscopy, which is an invasive procedure that causes discomfort in patients. The currently available non-invasive approaches either show limited sensitivity in low-grade tumours or possess unsatisfying specificity. The aim of the present study is to develop a new non-invasive strategy based on chromosomal imbalance levels to detect bladder cancer effectively. METHODS: We enrolled 74 patients diagnosed with bladder cancer (BC), 51 healthy participants and 27 patients who were diagnosed with non-malignant urinary disease (UD)...
June 15, 2018: BMC Cancer
Yipeng Wang, Liping Guo, Lin Feng, Wen Zhang, Ting Xiao, Xuebing Di, Guoji Chen, Kaitai Zhang
Circulating tumour cell (CTC) behaviours are distinct from those of bulk tissues. Thus, treatments to eliminate CTCs differ from the regimens followed to reduce the primary tumour and its metastases. Accordingly, comprehensively deciphering the single nucleotide variant (SNV) profiles in CTCs, which partially determine CTC behaviours, is a priority. Using viable CTCs isolated with the oHSV1‑hTERT‑GFP virus coupled with fluorescence‑activated cell sorting (FACS), the whole genome was amplified using the multiple annealing and looping‑based amplification cycle (MALBAC) method...
May 2018: Oncology Reports
Fei He, Wanjun Zhou, Ren Cai, Tizhen Yan, Xiangmin Xu
In this study, we aimed to assess the performance of two whole-genome amplification methods, multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycle (MALBAC), for β-thalassemia genotyping and single-nucleotide polymorphism (SNP)/copy-number variant (CNV) detection using two DNA sequencing assays. We collected peripheral blood, cell lines, and discarded embryos, and carried out MALBAC and MDA on single-cell and five-cell samples. We detected and statistically analyzed differences in the amplification efficiency, positive predictive value, sensitivity, allele dropout (ADO) rate, SNPs, and CV values between the two methods...
April 2018: Journal of Human Genetics
Wei Shang, Yunshan Zhang, Mingming Shu, Weizhou Wang, Likun Ren, Fu Chen, Lin Shao, Sijia Lu, Shiping Bo, Shujie Ma, Yumei Gao
Single cell whole genome sequencing helps to decipher the genome heterogeneity within a cell population and facilitates the analysis of trace amounts of genetic material, such as is found in human embryos. The mitochondrial genome, although an important part of the genetic composition of eukaryotic cells, is often neglected in single cell genome analysis. A recently developed single cell whole genome amplification method was used, known as multiple annealing and looping based amplification cycles (MALBAC-NGS), for simultaneous analysis of chromosomal and mitochondrial genomes at the single cell level...
January 2018: Reproductive Biomedicine Online
Carmela Paolillo, Zhaomei Mu, Giovanna Rossi, Matthew J Schiewer, Thomas Nguyen, Laura Austin, Ettore Capoluongo, Karen Knudsen, Massimo Cristofanilli, Paolo Fortina
Purpose: Early detection is essential for treatment plans before onset of metastatic disease. Our purpose was to demonstrate feasibility to detect and monitor estrogen receptor 1 ( ESR1 ) gene mutations at the single circulating tumor cell (CTC) level in metastatic breast cancer (MBC). Experimental Design: We used a CTC molecular characterization approach to investigate heterogeneity of 14 hotspot mutations in ESR1 and their correlation with endocrine resistance. Combining the CellSearch and DEPArray technologies allowed recovery of 71 single CTCs and 12 WBC from 3 ER-positive MBC patients...
October 15, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Shonan Sho, Colin M Court, Paul Winograd, Sangjun Lee, Shuang Hou, Thomas G Graeber, Hsian-Rong Tseng, James S Tomlinson
BACKGROUND: Sequencing analysis of circulating tumor cells (CTCs) enables "liquid biopsy" to guide precision oncology strategies. However, this requires low-template whole genome amplification (WGA) that is prone to errors and biases from uneven amplifications. Currently, quality control (QC) methods for WGA products, as well as the number of CTCs needed for reliable downstream sequencing, remain poorly defined. We sought to define strategies for selecting and generating optimal WGA products from low-template input as it relates to their potential applications in precision oncology strategies...
July 1, 2017: BMC Cancer
Xinyi Zhang, Bo Liang, Xiaoyan Xu, Feifei Zhou, Lingyin Kong, Jingjing Shen, Yingying Xia, Liming Xuan, Yan Mao, Yongfeng Xue, Caixia Liu, Jichun Tan
With the development and clinical application of genomics, more and more concern is focused on single-cell sequencing. In the process of single-cell sequencing, whole genome amplification is a key step to enrich sample DNA. Previous studies have compared the performance of different whole genome amplification (WGA) strategies on Illumina sequencing platforms, but there is no related research aimed at Ion Proton platform, which is also a popular next-generation sequencing platform. Here by amplifying cells from six cell lines with different karyotypes, we estimated the data features of four common commercial WGA kits (PicoPLEX WGA Kit, GenomePlex Single Cell Whole Genome Amplification Kit, MALBAC Single Cell Whole Genome Amplification Kit, and REPLI-g Single Cell Kit), including median absolute pairwise difference, uniformity, reproducibility, and fidelity, and examined their performance of copy number variation detection...
August 31, 2017: Bioscience Reports
WeiQiang Liu, HuiMin Zhang, Dan Hu, SiJia Lu, XiaoFang Sun
AIM: To select an optimal whole-genome amplification (WGA) method to improve the efficiency of the preimplantation genetic diagnosis and screening (PGD/PGS) of beta-thalassaemia disorders. METHODS: Fifty-seven fibroblast samples with defined beta-thalassaemia variations and forty-eight single-blastomere samples were amplified from single-, two-, and five-cell samples by multiple annealing and looping-based amplification cycles (MALBAC) and the multiple displacement amplification (MDA) method...
February 2018: Journal of Clinical Laboratory Analysis
Erik Borgström, Marta Paterlini, Jeff E Mold, Jonas Frisen, Joakim Lundeberg
BACKGROUND: Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly. RESULTS: The largest difference between the evaluated protocols was observed when analyzing the target coverage and read depth distribution. These differences also had impact on the downstream variant calling...
2017: PloS One
Jiawei Xu, Wenbin Niu, Zhaofeng Peng, Xiao Bao, Meixiang Zhang, Linlin Wang, Linqing Du, Nan Zhang, Yingpu Sun
Triploidy occurred about 2-3% in human pregnancies and contributed to approximately 15% of chromosomally caused human early miscarriage. It is essential for preimplantation genetic diagnosis and screen to distinct triploidy sensitively. Here, we performed comparative investigations between MALBAC-NGS and MDA-SNP array sensitivity on triploidy detection. Self-correction and reference-correction algorism were used to analyze the NGS data. We identified 5 triploid embryos in 1198 embryos of 218 PGD and PGS cycles using MDA-SNP array, the rate of tripoidy was 4...
December 6, 2016: Oncotarget
Juanjuan Xu, Rui Fang, Li Chen, Daozhen Chen, Jian-Ping Xiao, Weimin Yang, Honghua Wang, Xiaoqing Song, Ting Ma, Shiping Bo, Chong Shi, Jun Ren, Lei Huang, Li-Yi Cai, Bing Yao, X Sunney Xie, Sijia Lu
Preimplantation genetic screening (PGS) is widely used to select in vitro-fertilized embryos free of chromosomal abnormalities and to improve the clinical outcome of in vitro fertilization (IVF). A disadvantage of PGS is that it requires biopsy of the preimplantation human embryo, which can limit the clinical applicability of PGS due to the invasiveness and complexity of the process. Here, we present and validate a noninvasive chromosome screening (NICS) method based on sequencing the genomic DNA secreted into the culture medium from the human blastocyst...
October 18, 2016: Proceedings of the National Academy of Sciences of the United States of America
Jin Huang, Liying Yan, Sijia Lu, Nan Zhao, X Sunney Xie, Jie Qiao
OBJECTIVE: To validate a 24-chromosome aneuploidy preimplantation genetic screening protocol based on multiple annealing and looping-based amplification cycle (MALBAC) and next-generation sequencing (NGS). DESIGN: Single-nucleotide polymorphism (SNP) array and MALBAC-NGS analysis. SETTING: University-affiliated in vitro fertilization (IVF) center. PATIENT(S): Fifteen women from whom 30 blastocysts were obtained for genotyping...
June 2016: Fertility and Sterility
Liying Yan, Lei Huang, Liya Xu, Jin Huang, Fei Ma, Xiaohui Zhu, Yaqiong Tang, Mingshan Liu, Ying Lian, Ping Liu, Rong Li, Sijia Lu, Fuchou Tang, Jie Qiao, X Sunney Xie
In vitro fertilization (IVF), preimplantation genetic diagnosis (PGD), and preimplantation genetic screening (PGS) help patients to select embryos free of monogenic diseases and aneuploidy (chromosome abnormality). Next-generation sequencing (NGS) methods, while experiencing a rapid cost reduction, have improved the precision of PGD/PGS. However, the precision of PGD has been limited by the false-positive and false-negative single-nucleotide variations (SNVs), which are not acceptable in IVF and can be circumvented by linkage analyses, such as short tandem repeats or karyomapping...
December 29, 2015: Proceedings of the National Academy of Sciences of the United States of America
Yong Hou, Kui Wu, Xulian Shi, Fuqiang Li, Luting Song, Hanjie Wu, Michael Dean, Guibo Li, Shirley Tsang, Runze Jiang, Xiaolong Zhang, Bo Li, Geng Liu, Niharika Bedekar, Na Lu, Guoyun Xie, Han Liang, Liao Chang, Ting Wang, Jianghao Chen, Yingrui Li, Xiuqing Zhang, Huanming Yang, Xun Xu, Ling Wang, Jun Wang
BACKGROUND: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). However, a comprehensive comparison of variations detection performance between these WGA methods has not yet been performed...
2015: GigaScience
Lieselot Deleye, Dieter De Coninck, Christodoulos Christodoulou, Tom Sante, Annelies Dheedene, Björn Heindryckx, Etienne Van den Abbeel, Petra De Sutter, Björn Menten, Dieter Deforce, Filip Van Nieuwerburgh
Current whole genome amplification (WGA) methods lead to amplification bias resulting in over- and under-represented regions in the genome. Nevertheless, certain WGA methods, such as SurePlex and subsequent arrayCGH analysis, make it possible to detect copy number alterations (CNAs) at a 10 Mb resolution. A more uniform WGA combined with massive parallel sequencing (MPS), however, could allow detection at higher resolution and lower cost. Recently, MALBAC, a new WGA method, claims unparalleled performance...
2015: Scientific Reports
Luwen Ning, Zhoufang Li, Guan Wang, Wen Hu, Qingming Hou, Yin Tong, Meng Zhang, Yao Chen, Li Qin, Xiaoping Chen, Heng-Ye Man, Pinghua Liu, Jiankui He
Single-cell genomic analysis has grown rapidly in recent years and finds widespread applications in various fields of biology, including cancer biology, development, immunology, pre-implantation genetic diagnosis, and neurobiology. To date, the amplification bias, amplification uniformity and reproducibility of the three major single cell whole genome amplification methods (GenomePlex WGA4, MDA and MALBAC) have not been systematically investigated using mammalian cells. In this study, we amplified genomic DNA from individual hippocampal neurons using three single-cell DNA amplification methods, and sequenced them at shallow depth...
June 19, 2015: Scientific Reports
Lei Huang, Fei Ma, Alec Chapman, Sijia Lu, Xiaoliang Sunney Xie
We present a survey of single-cell whole-genome amplification (WGA) methods, including degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycles (MALBAC). The key parameters to characterize the performance of these methods are defined, including genome coverage, uniformity, reproducibility, unmappable rates, chimera rates, allele dropout rates, false positive rates for calling single-nucleotide variations, and ability to call copy-number variations...
2015: Annual Review of Genomics and Human Genetics
Na Li, Li Wang, Hui Wang, Minyue Ma, Xiaohong Wang, Yi Li, Wenke Zhang, Jianguang Zhang, David S Cram, Yuanqing Yao
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 (15 pg) 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...
April 20, 2015: Journal of Genetics and Genomics, Yi Chuan Xue Bao
Cheng-Zhong Zhang, Viktor A Adalsteinsson, Joshua Francis, Hauke Cornils, Joonil Jung, Cecile Maire, Keith L Ligon, Matthew Meyerson, J Christopher Love
Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1-10 kb)...
April 16, 2015: Nature Communications
Minfeng Chen, Pengfei Song, Dan Zou, Xuesong Hu, Shancen Zhao, Shengjie Gao, Fei Ling
[This corrects the article DOI: 10.1371/journal.pone.0114520.].
2015: PloS One
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