keyword
MENU ▼
Read by QxMD icon Read
search

MALBAC

keyword
https://www.readbyqxmd.com/read/29203383/comprehensive-chromosomal-and-mitochondrial-copy-number-profiling-in-human-ivf-embryos
#1
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...
November 8, 2017: Reproductive Biomedicine Online
https://www.readbyqxmd.com/read/28679775/detection-of-activating-estrogen-receptor-gene-esr1-mutations-in-single-circulating-tumor-cells
#2
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
https://www.readbyqxmd.com/read/28666423/precision-oncology-using-a-limited-number-of-cells-optimization-of-whole-genome-amplification-products-for-sequencing-applications
#3
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
https://www.readbyqxmd.com/read/28572171/the-comparison-of-the-performance-of-four-whole-genome-amplification-kits-on-ion-proton-platform-in-copy-number-variation-detection
#4
Xinyi Zhang, Bo Liang, Xiaoyan Xu, Feifei Zhou, Lingyin Kong, Jingjing Shen, Yingying Xia, Liming Xuan, Yan Mao, Yongfeng Xue, 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 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...
June 1, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28548214/the-performance-of-malbac-and-mda-methods-in-the-identification-of-concurrent-mutations-and-aneuploidy-screening-to-diagnose-beta-thalassaemia-disorders-at-the-single-and-multiple-cell-levels
#5
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...
May 26, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28207771/comparison-of-whole-genome-amplification-techniques-for-human-single-cell-exome-sequencing
#6
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
https://www.readbyqxmd.com/read/27833086/comparative-study-of-single-nucleotide-polymorphism-array-and-next-generation-sequencing-based-strategies-on-triploid-identification-in-preimplantation-genetic-diagnosis-and-screen
#7
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
https://www.readbyqxmd.com/read/27688762/noninvasive-chromosome-screening-of-human-embryos-by-genome-sequencing-of-embryo-culture-medium-for-in-vitro-fertilization
#8
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
https://www.readbyqxmd.com/read/26902859/validation-of-a-next-generation-sequencing-based-protocol-for-24-chromosome-aneuploidy-screening-of-blastocysts
#9
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
https://www.readbyqxmd.com/read/26712022/live-births-after-simultaneous-avoidance-of-monogenic-diseases-and-chromosome-abnormality-by-next-generation-sequencing-with-linkage-analyses
#10
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
https://www.readbyqxmd.com/read/26251698/comparison-of-variations-detection-between-whole-genome-amplification-methods-used-in-single-cell-resequencing
#11
COMPARATIVE STUDY
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
https://www.readbyqxmd.com/read/26122179/whole-genome-amplification-with-sureplex-results-in-better-copy-number-alteration-detection-using-sequencing-data-compared-to-the-malbac-method
#12
COMPARATIVE STUDY
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
https://www.readbyqxmd.com/read/26091148/quantitative-assessment-of-single-cell-whole-genome-amplification-methods-for-detecting-copy-number-variation-using-hippocampal-neurons
#13
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
https://www.readbyqxmd.com/read/26077818/single-cell-whole-genome-amplification-and-sequencing-methodology-and-applications
#14
REVIEW
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
https://www.readbyqxmd.com/read/25953353/the-performance-of-whole-genome-amplification-methods-and%C3%A2-next-generation-sequencing-for-pre-implantation-genetic-diagnosis-of-chromosomal-abnormalities
#15
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
https://www.readbyqxmd.com/read/25879913/calibrating-genomic-and-allelic-coverage-bias-in-single-cell-sequencing
#16
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
https://www.readbyqxmd.com/read/25875279/correction-comparison-of-multiple-displacement-amplification-mda-and-multiple-annealing-and-looping-based-amplification-cycles-malbac-in-single-cell-sequencing
#17
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
https://www.readbyqxmd.com/read/25822772/single-cell-transcriptome-amplification-with-malbac
#18
Alec R Chapman, Zi He, Sijia Lu, Jun Yong, Longzhi Tan, Fuchou Tang, X Sunney Xie
Recently, Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) has been developed for whole genome amplification of an individual cell, relying on quasilinear instead of exponential amplification to achieve high coverage. Here we adapt MALBAC for single-cell transcriptome amplification, which gives consistently high detection efficiency, accuracy and reproducibility. With this newly developed technique, we successfully amplified and sequenced single cells from 3 germ layers from mouse embryos in the early gastrulation stage, and examined the epithelial-mesenchymal transition (EMT) program among cells in the mesoderm layer on a single-cell level...
2015: PloS One
https://www.readbyqxmd.com/read/25485707/comparison-of-multiple-displacement-amplification-mda-and-multiple-annealing-and-looping-based-amplification-cycles-malbac-in-single-cell-sequencing
#19
COMPARATIVE STUDY
Minfeng Chen, Pengfei Song, Dan Zou, Xuesong Hu, Shancen Zhao, Shengjie Gao, Fei Ling
Single-cell sequencing promotes our understanding of the heterogeneity of cellular populations, including the haplotypes and genomic variability among different generation of cells. Whole-genome amplification is crucial to generate sufficient DNA fragments for single-cell sequencing projects. Using sequencing data from single sperms, we quantitatively compare two prevailing amplification methods that extensively applied in single-cell sequencing, multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC)...
2014: PloS One
https://www.readbyqxmd.com/read/25241375/validation-of-multiple-annealing-and-looping-based-amplification-cycle-sequencing-for-24-chromosome-aneuploidy-screening-of-cleavage-stage-embryos
#20
Jin Huang, Liying Yan, Wei Fan, Nan Zhao, Yan Zhang, Fuchou Tang, X Sunney Xie, Jie Qiao
OBJECTIVE: To validate multiple annealing and looping-based amplification cycle (MALBAC) sequencing for 24-chromosome aneuploidy screening of cleavage embryos and to explore the chromosomal characteristics of embryos at the cleavage stage. DESIGN: The 24-chromosome aneuploidy analyses of the blastomeres included comparative genomic hybridization (CGH), single nucleotide polymorphism (SNP), and MALBAC sequencing. SETTING: University-affiliated IVF center...
December 2014: Fertility and Sterility
keyword
keyword
3457
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"