Single-cell chromosomal imbalances detection by array CGH

Caignec, Cédric Le; Spits, Claudia; Sermon, Karen; Rycke, Martine De; Thienpont, Bernard; Debrock, Sophie; Staessen, Cathérine; Moreau, Yves; Fryns, Jean‐Pierre; Steirteghem, André Van; Liebaers, Inge; Vermeesch, Joris Robert

doi:10.1093/nar/gkl336

Cited by 189 publications

(129 citation statements)

References 33 publications

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“…Multiple aCGH experiments[36, 37], and recently a MPS experiment[104], have used single-cell approaches to profile CNVs in individual human normal and tumor cells, but base-pair resolution genotyping of single eukaryotic cells has not yet been shown. Massively parallel sequencing of single-cells has the potential to revolutionize reproductive medicine, cancer research, developmental biology and aging research.…”

Section: Mps Applications In Mutation Analysismentioning

confidence: 99%

Direct mutation analysis by high-throughput sequencing: From germline to low-abundant, somatic variants

Gundry

Vijg

2012

Mutation Research/Fundamental and Molecular Mechanisms of Mutag

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DNA mutations are the source of genetic variation within populations. The majority of mutations with observable effects are deleterious. In humans mutations in the germ line can cause genetic disease. In somatic cells multiple rounds of mutations and selection lead to cancer. The study of genetic variation has progressed rapidly since the completion of the draft sequence of the human genome. Recent advances in sequencing technology, most importantly the introduction of massively parallel sequencing (MPS), have resulted in more than a hundred-fold reduction in the time and cost required for sequencing nucleic acids. These improvements have greatly expanded the use of sequencing as a practical tool for mutation analysis. While in the past the high cost of sequencing limited mutation analysis to selectable markers or small forward mutation targets assumed to be representative for the genome overall, current platforms allow whole genome sequencing for less than $5,000. This has already given rise to direct estimates of germline mutation rates in multiple organisms including humans by comparing whole genome sequences between parents and offspring. Here we present a brief history of the field of mutation research, with a focus on classical tools for the measurement of mutation rates. We then review MPS, how it is currently applied and the new insight into human and animal mutation frequencies and spectra that has been obtained from whole genome sequencing. While great progress has been made, we note that the single most important limitation of current MPS approaches for mutation analysis is the inability to address low-abundance mutations that turn somatic tissues into mosaics of cells. Such mutations are at the basis of intra-tumor heterogeneity, with important implications for clinical diagnosis, and could also contribute to somatic diseases other than cancer, including aging. Some possible approaches to gain access to low-abundance mutations are discussed, with a brief overview of new sequencing platforms that are currently waiting in the wings to advance this exploding field even further.

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Section: Mps Applications In Mutation Analysismentioning

confidence: 99%

Direct mutation analysis by high-throughput sequencing: From germline to low-abundant, somatic variants

Gundry

Vijg

2012

Mutation Research/Fundamental and Molecular Mechanisms of Mutag

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“…Major advantages of the array-based cytogenetic technologies are the high resolution and high throughput (Salman et al, 2004). It also offers new possibilities for genetic pre-implantation analysis, opening the route toward aneuploidy screening and detection of unbalanced translocations in embryos (Le Caignec et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Array-CGH testing in spontaneous abortions with normal karyotypes

Borovik

Pérez²,

Silva

et al. 2008

Genet. Mol. Biol.

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In about 50% of first trimester spontaneous abortion the cause remains undetermined after standard cytogenetic investigation. We evaluated the usefulness of array-CGH in diagnosing chromosome abnormalities in products of conception from first trimester spontaneous abortions. Cell culture was carried out in short-and long-term cultures of 54 specimens and cytogenetic analysis was successful in 49 of them. Cytogenetic abnormalities (numerical and structural) were detected in 22 (44.89%) specimens. Subsequent, array-CGH based on large insert clones spaced at 1 Mb intervals over the whole genome was used in 17 cases with normal G-banding karyotype. This revealed chromosome aneuplodies in three additional cases, giving a final total of 51% cases in which an abnormal karyotype was detected. In keeping with other recently published works, this study shows that array-CGH detects abnormalities in a further~10% of spontaneous abortion specimens considered to be normal using standard cytogenetic methods. As such, array-CGH technique may present a suitable complementary test to cytogenetic analysis in cases with a normal karyotype.

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“…The euploid samples had an average of 5.00 informative SNPs (range 1-11), and 23 of these (8.3%) had only 1 or 2 informative SNPs. In contrast, trisomy 21 samples had an average of 7.58 informative SNPs (range [3][4][5][6][7][8][9][10][11], and none of these had Ͻ3 informative SNPs. This difference may have contributed to the increased number of probable unaffected calls within the nontrisomy 21 samples.…”

Section: Resultsmentioning

confidence: 99%

“…6 Array CGH has been recently shown to be able to detect abnormalities in chromosome number, including trisomy 13, 18 and 21 and monosomy X, from cell-free DNA from amniotic fluid supernatant as well as single cells. [7][8][9] Extensive work has been performed on molecular methods making use of frequently occurring genetic loci such as short tandem repeats (STR) or single nucleotide polymorphisms (SNP) to analyze chromosome number. One method which is currently being used in some European countries is quantitative fluorescent polymerase chain reaction (QF-PCR) analysis of STRs.…”

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confidence: 99%

Reliable detection of Trisomy 21 using MALDI-TOF mass spectrometry

Huang

Nelson

Zimmermann

et al. 2006

Genetics in Medicine

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Purpose: Current diagnostic methods for chromosomal abnormalities rely mainly on karyotyping and occasionally fluorescent in situ hybridization or quantitative polymerase chain reaction . We describe an alternative molecular method for the detection of trisomy 21 involving mass spectrometric analysis of single nucleotide polymorphisms.Methods: In collaboration with Sequenom, Inc., 350 blinded amniotic fluid, amniocyte culture, chorionic villus, or amniotic fluid supernatant samples were analyzed for trisomy 21 using SNP analysis and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Peak ratios were calculated for heterozygous genotypes and compared to control values generated from known euploid samples. An analytical algorithm using standard deviations from control values was used to determine the probability of a sample being affected or

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Single-cell chromosomal imbalances detection by array CGH

Cited by 189 publications

References 33 publications

Direct mutation analysis by high-throughput sequencing: From germline to low-abundant, somatic variants

Direct mutation analysis by high-throughput sequencing: From germline to low-abundant, somatic variants

Array-CGH testing in spontaneous abortions with normal karyotypes

Reliable detection of Trisomy 21 using MALDI-TOF mass spectrometry

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