Single-cell copy number varation detection: blastomeres
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Jiqiu Cheng
PROVIDER: E-GEOD-31219 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Detection of genomic rearrangements from a single cell instead of a population of cells is an emerging research technique with important applications in the study of human fertility, constitutional chromosomal disorders, and tumor progression. Here, we develop a method to improve the detection of single-cell genome-wide copy number variation. At this study, 7 amplified single cell DNA samples derived from EBV-line [47,XY,+21], [46,XY,der(20),t(18;20)(p11.21;p13)], [46,XX,del(18)(p11.21->pter)], [46,X,der(X),t(X;14)(q21.1;q12.2)] were analyzed by Agilent 244K array CGH. For these single cell Agilent 244K array CGH analyses: non-amplified genomic DNA extracted from the blood of a Klinefelter patient (XXY) was used as a reference sample. As a validation, the corresponding non-amplified genomic DNA samples were analyzed by 250K Nsp I SNP arrays (platform GPL3718). Non-amplified genomic DNA extracted from the blood of a Klinefelter patient (XXY) was used as a reference sample for BAC array CGH
2011-08-23 | E-GEOD-27892 | biostudies-arrayexpress
Project description:A method to infer genome-wide haplotypes from the analysis of one or two single (human) cells has tremendous applicative value. It would revolutionize not only preimplantation genetic diagnosis of in vitro fertilized human embryos in the clinic, but also animal breeding programs by enabling genome-wide quantitative trait loci selection at the embryonic level. In addition, it allows to further scrutinize drivers of haplotype diversity, mainly meiotic homologous recombination as well as somatic (homologous) recombination processes that occur often during (human) tumorigenesis. We developed a generic approach to type genome-wide single nucleotide polymorphisms in single human cells and to reconstruct genome-wide haplotypes of single or dual cell derived genotypes. Genome-wide sequences of syntenic alleles were determined for EBV-transformed lymphoblastoid cells as well as human blastomeres. To this end, multiple displacement amplified DNA samples of single cells were hybridized to Affymetrix 250K SNP-arrays. Different algorithmic designs were subsequently developed to assess from the single cell-derived SNP-probe intensities the sequence of syntenic alleles and to pinpoint accurately the majority of parental homologous recombination sites using a linkage-based approach. In total 12 amplified single human lymphoblastoid cell DNA samples, 3 amplified single human blastomere DNA samples and 19 non-amplified genomic DNA samples extracted from blood were analyzed by 250K Nsp I SNP arrays (GEO accession number GPL3718). The non-amplified genomic DNA samples extracted from blood were derived from 19 different persons belonging to 4 different families. The sample names of these 19 samples are respectively Family1_Individual1, Family1_mother, Family1_father, Family1_MaternalGrandmother, Family2_Individual2, Family2_mother, Family2_father, Family2_MaternalGrandmother, Family2_MaternalGrandfather, Family3_Individual3, Family3_Individual4, Family3_mother, Family3_father, Family3_MaternalGrandmother, Family3_MaternalGrandfather, Family4_mother, Family4_father, Family4_PaternalGrandmother, Family4_PaternalGrandfather. These 19 non-amplified genomic DNA samples extracted from blood were genotyped using the dynamic model algorithm embedded in the M-bM-^@M-^XGeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)M-bM-^@M-^Y using a homozygous and heterozygous calling threshold of 0.12. The 12 amplified single lymphoblastoid cell DNA samples were derived from Epstein Barr virus transformed lymphoblastoid cell lines (EBV-line) of four different persons. Three amplified single lymphoblastoid cell DNA samples from individual M-bM-^@M-^\Family1_Individual1M-bM-^@M-^], three amplified single lymphoblastoid cell DNA samples from individual M-bM-^@M-^\Family2_Individual2M-bM-^@M-^], three amplified single lymphoblastoid cell DNA samples from individual M-bM-^@M-^\Family3_Individual3M-bM-^@M-^] and three amplified single lymphoblastoid cell DNA samples from individual M-bM-^@M-^\Family3_Individual4M-bM-^@M-^]. The samples names of these 12 are respectively: Family1_Individual1_SingleCell1, Family1_Individual1_SingleCell2, Family1_Individual1_SingleCell3, Family2_Individual2_SingleCell1, Family2_Individual2_SingleCell2, Family2_Individual2_SingleCell3, Family3_Individual3_SingleCell1, Family3_Individual3_SingleCell2, Family3_Individual3_SingleCell3, Family3_Individual4_SingleCell1, Family3_Individual4_SingleCell2, Family3_Individual4_SingleCell3. These 12 amplified single lymphoblastoid cell DNA samples were genotyped using (1) the dynamic model algorithm embedded in the M-bM-^@M-^XGeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)M-bM-^@M-^Y using a homozygous and heterozygous calling threshold of 0.12, (2) the BRLMM algorithm within the M-bM-^@M-^XGenotyping console 3.0.1M-bM-^@M-^Y software (Affymetrix) using a scoring threshold of 0.1 and (3) the Birdseed algorithm of the APT-1.10.1 package (Affymetrix Power Tools) using the M-bM-^@M-^Xbirdseed-devM-bM-^@M-^Y command which is the most recently incorporated development version of birdseed from The Broad Institute (http://www.broadinstitute.org/mpg/birdsuite/birdseed.html). The 3 amplified single human blastomere DNA samples were derived from three different human blastomeres that belong to the same in vitro fertilized embryo. This embryo was conceived in vitro by using sperm of person M-bM-^@M-^\Family4_fatherM-bM-^@M-^] and an oocyte from person M-bM-^@M-^\Family4_motherM-bM-^@M-^]. The sample names of these 3 amplified single blastomere DNA samples are respectively: Family4_Blastomere1, Family4_Blastomere2, Family4_Blastomere3. These 3 amplified single human blastomere DNA samples were genotyped using the dynamic model algorithm embedded in the M-bM-^@M-^XGeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)M-bM-^@M-^Y using a homozygous and heterozygous calling threshold of 0.12.
2012-10-01 | E-GEOD-17318 | biostudies-arrayexpress
Project description:Methods for haplotyping and DNA copy number typing of single cells are paramount for studying genomic heterogeneity and enabling genetic diagnosis. Before analyzing the DNA of a single cell by microarray or next-generation sequencing, a whole-genome amplification (WGA) process is required that substantially distorts the frequency and composition of the cell’s alleles. As a consequence, haplotyping methods suffer from error-prone discrete SNP-genotypes (AA, AB, BB), and DNA copy number profiling remains difficult as true DNA copy number aberrations have to be discriminated from WGA-artifacts. Here, we developed a single-cell genome analysis method that reconstructs genome-wide haplotype architectures as well as the copy-number and segregational origin of those haplotypes by deciphering WGA-distorted SNP B-allele fractions, using a process we coin haplarithmisis. We demonstrate clinical precision of the method on single cells biopsied from human embryos to diagnose disease alleles genome wide, we advance and facilitate the detection of numerical and structural chromosomal anomalies in single cells, and can distinguish meiotic from mitotic segregation errors in a single assay. The samples of a reference family were applied for optimisation of single-cell genotyping using Affymetrix SNP-arrays prior to downstream analysis. Specifically, the reference family delivers genomic DNA samples isolated from peripheral blood of two siblings 'S1' and 'S2', the mother and father of these siblings, as well as of the maternal grandmother and grandfather. Of individuals ‘S1’ and ‘S2’, six EBV-transformed lymphoblastoid single cells were isolated of which three were whole-genome amplified using MDA and three using PicoPlex. These WGA-products were hybridized to Affymetrix NspI 250K SNP-arrays following the protocol as recommended by the company. Subsequently, the SNP-probe signals were interpreted by different genotyping algorithms (see data processing). Based on overall performance, it was decided to use the Dynamic Model (DM) for interpreting Affymetrix SNP-probe signals of single cells.
2015-05-15 | E-GEOD-60907 | biostudies-arrayexpress
Project description:Seventy blastomeres from fourteen frozen-thawed supernumerary human preimplantation embryos were disassociated and genomic was amplified using Multiple Displacement Amplification. BAC array-CGH was performed on the amplified products. BAC array-CGH on single blastomeres amplified by Multiple Displacement Amplification.
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2012-01-01 | E-GEOD-32567 | biostudies-arrayexpress
Project description:ChIP-chip study using embryonic E18.5 mouse kidney tissue and anti-WT1 antibody (Santa Cruz C19 and N180) performed in three technical replicates. ChIP DNA was not PCR amplified prior to hybridization to Agilent 244K mouse promoter arrays, to avoid potential PCR amplification bias.
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Project description:CGH microarray in a patient with variant APL 1 sample hybridized to the Whole Human Genome CGH microarray 244K
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