The Experts below are selected from a list of 21408 Experts worldwide ranked by ideXlab platform
Irene Netchine - One of the best experts on this subject based on the ideXlab platform.
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formation of upd 7 mat by trisomic rescue SNP Array typing provides new insights in chromosomal nondisjunction
Molecular Cytogenetics, 2017Co-Authors: Sandra Chantotbastaraud, Svea Stratma, Frederic Ioude, Matthias Egema, Miriam Elbrach, Luitgard Graulneuma, Madeleine D Harbiso, Irene NetchineAbstract:Maternal uniparental disomy (UPD) of chromosome 7 (upd(7)mat) accounts for approximately 10% of patients with Silver-Russell syndrome (SRS). For upd(7)mat and trisomy 7, a significant number of mechanisms have been proposed to explain the postzygotic formation of these chromosomal compositions, but all have been based on as small number of cases. To obtain the ratio of isodisomy and heterodisomy in UPDs (hUPD, iUPD) and to determine the underlying formation mechanisms, we analysed a large cohort of upd(7)mat patients (n = 73) by SNP Array typing. Based on these data, we discuss the UPDs and their underlying trisomy 7 formation mechanisms. A whole chromosome 7 maternal iUPD was confirmed in 28.8%, a mixture or complete maternal hUPD in 71.2% of patients. We could demonstrate that nondisjunction mechanism affecting chromosome 7 are similar to that of the chromosomes more frequently involved in trisomy (and/or UPD), and that mechanisms other than trisomic rescue have a lower significance than previously suspected. Furthermore, we suggest SNP Array typing for future parent- and cell-stage-of origin studies in human aneuploidies as they allow the definite classification of trisomies and UPDs, and provide information on recombinational events and their suggested association with aneuploidy formation.
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Formation of upd(7)mat by trisomic rescue: SNP Array typing provides new insights in chromosomal nondisjunction
BMC, 2017Co-Authors: Sandra Chantot-bastaraud, Svea Stratma, Frederic Ioude, Matthias Egema, Miriam Elbrach, Madeleine D Harbiso, Irene Netchine, Luitgard Graul-neuma, Thomas EggermaAbstract:Abstract Background Maternal uniparental disomy (UPD) of chromosome 7 (upd(7)mat) accounts for approximately 10% of patients with Silver-Russell syndrome (SRS). For upd(7)mat and trisomy 7, a significant number of mechanisms have been proposed to explain the postzygotic formation of these chromosomal compositions, but all have been based on as small number of cases. To obtain the ratio of isodisomy and heterodisomy in UPDs (hUPD, iUPD) and to determine the underlying formation mechanisms, we analysed a large cohort of upd(7)mat patients (n = 73) by SNP Array typing. Based on these data, we discuss the UPDs and their underlying trisomy 7 formation mechanisms. Results A whole chromosome 7 maternal iUPD was confirmed in 28.8%, a mixture or complete maternal hUPD in 71.2% of patients. Conclusions We could demonstrate that nondisjunction mechanism affecting chromosome 7 are similar to that of the chromosomes more frequently involved in trisomy (and/or UPD), and that mechanisms other than trisomic rescue have a lower significance than previously suspected. Furthermore, we suggest SNP Array typing for future parent- and cell-stage-of origin studies in human aneuploidies as they allow the definite classification of trisomies and UPDs, and provide information on recombinational events and their suggested association with aneuploidy formation
Trevor A. Graham - One of the best experts on this subject based on the ideXlab platform.
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Quantification of within-sample genetic heterogeneity from SNP-Array data
Scientific reports, 2017Co-Authors: Pierre Martinez, Christopher Kimberley, Nicolai Juul Birkbak, Andrea Marion Marquard, Zoltan Szallasi, Trevor A. GrahamAbstract:Intra-tumour genetic heterogeneity (ITH) fosters drug resistance and is a critical hurdle to clinical treatment. ITH can be well-measured using multi-region sampling but this is costly and challenging to implement. There is therefore a need for tools to estimate ITH in individual samples, using standard genomic data such as SNP-Arrays, that could be implemented routinely. We designed two novel scores S and R, respectively based on the Shannon diversity index and Ripley’s L statistic of spatial homogeneity, to quantify ITH in single SNP-Array samples. We created in-silico and in-vitro mixtures of tumour clones, in which diversity was known for benchmarking purposes. We found significant but highly-variable associations of our scores with diversity in-silico (p
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quantification of within sample genetic heterogeneity from SNP Array data
Scientific Reports, 2017Co-Authors: Pierre Martinez, Christopher Kimberley, Nicolai Juul Birkbak, Andrea Marion Marquard, Zoltan Szallasi, Trevor A. GrahamAbstract:Intra-tumour genetic heterogeneity (ITH) fosters drug resistance and is a critical hurdle to clinical treatment. ITH can be well-measured using multi-region sampling but this is costly and challenging to implement. There is therefore a need for tools to estimate ITH in individual samples, using standard genomic data such as SNP-Arrays, that could be implemented routinely. We designed two novel scores S and R, respectively based on the Shannon diversity index and Ripley’s L statistic of spatial homogeneity, to quantify ITH in single SNP-Array samples. We created in-silico and in-vitro mixtures of tumour clones, in which diversity was known for benchmarking purposes. We found significant but highly-variable associations of our scores with diversity in-silico (p < 0.001) and moderate associations in–vitro (p = 0.015 and p = 0.085). Our scores were also correlated to previous ITH estimates from sequencing data but heterogeneity in the fraction of tumour cells present across samples hampered accurate quantification. The prognostic potential of both scores was moderate but significantly predictive of survival in several tumour types (corrected p = 0.03). Our work thus shows how individual SNP-Arrays reveal intra-sample clonal diversity with moderate accuracy.
Pierre Martinez - One of the best experts on this subject based on the ideXlab platform.
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Quantification of within-sample genetic heterogeneity from SNP-Array data
Scientific reports, 2017Co-Authors: Pierre Martinez, Christopher Kimberley, Nicolai Juul Birkbak, Andrea Marion Marquard, Zoltan Szallasi, Trevor A. GrahamAbstract:Intra-tumour genetic heterogeneity (ITH) fosters drug resistance and is a critical hurdle to clinical treatment. ITH can be well-measured using multi-region sampling but this is costly and challenging to implement. There is therefore a need for tools to estimate ITH in individual samples, using standard genomic data such as SNP-Arrays, that could be implemented routinely. We designed two novel scores S and R, respectively based on the Shannon diversity index and Ripley’s L statistic of spatial homogeneity, to quantify ITH in single SNP-Array samples. We created in-silico and in-vitro mixtures of tumour clones, in which diversity was known for benchmarking purposes. We found significant but highly-variable associations of our scores with diversity in-silico (p
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quantification of within sample genetic heterogeneity from SNP Array data
Scientific Reports, 2017Co-Authors: Pierre Martinez, Christopher Kimberley, Nicolai Juul Birkbak, Andrea Marion Marquard, Zoltan Szallasi, Trevor A. GrahamAbstract:Intra-tumour genetic heterogeneity (ITH) fosters drug resistance and is a critical hurdle to clinical treatment. ITH can be well-measured using multi-region sampling but this is costly and challenging to implement. There is therefore a need for tools to estimate ITH in individual samples, using standard genomic data such as SNP-Arrays, that could be implemented routinely. We designed two novel scores S and R, respectively based on the Shannon diversity index and Ripley’s L statistic of spatial homogeneity, to quantify ITH in single SNP-Array samples. We created in-silico and in-vitro mixtures of tumour clones, in which diversity was known for benchmarking purposes. We found significant but highly-variable associations of our scores with diversity in-silico (p < 0.001) and moderate associations in–vitro (p = 0.015 and p = 0.085). Our scores were also correlated to previous ITH estimates from sequencing data but heterogeneity in the fraction of tumour cells present across samples hampered accurate quantification. The prognostic potential of both scores was moderate but significantly predictive of survival in several tumour types (corrected p = 0.03). Our work thus shows how individual SNP-Arrays reveal intra-sample clonal diversity with moderate accuracy.
Frederic Ioude - One of the best experts on this subject based on the ideXlab platform.
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formation of upd 7 mat by trisomic rescue SNP Array typing provides new insights in chromosomal nondisjunction
Molecular Cytogenetics, 2017Co-Authors: Sandra Chantotbastaraud, Svea Stratma, Frederic Ioude, Matthias Egema, Miriam Elbrach, Luitgard Graulneuma, Madeleine D Harbiso, Irene NetchineAbstract:Maternal uniparental disomy (UPD) of chromosome 7 (upd(7)mat) accounts for approximately 10% of patients with Silver-Russell syndrome (SRS). For upd(7)mat and trisomy 7, a significant number of mechanisms have been proposed to explain the postzygotic formation of these chromosomal compositions, but all have been based on as small number of cases. To obtain the ratio of isodisomy and heterodisomy in UPDs (hUPD, iUPD) and to determine the underlying formation mechanisms, we analysed a large cohort of upd(7)mat patients (n = 73) by SNP Array typing. Based on these data, we discuss the UPDs and their underlying trisomy 7 formation mechanisms. A whole chromosome 7 maternal iUPD was confirmed in 28.8%, a mixture or complete maternal hUPD in 71.2% of patients. We could demonstrate that nondisjunction mechanism affecting chromosome 7 are similar to that of the chromosomes more frequently involved in trisomy (and/or UPD), and that mechanisms other than trisomic rescue have a lower significance than previously suspected. Furthermore, we suggest SNP Array typing for future parent- and cell-stage-of origin studies in human aneuploidies as they allow the definite classification of trisomies and UPDs, and provide information on recombinational events and their suggested association with aneuploidy formation.
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Formation of upd(7)mat by trisomic rescue: SNP Array typing provides new insights in chromosomal nondisjunction
BMC, 2017Co-Authors: Sandra Chantot-bastaraud, Svea Stratma, Frederic Ioude, Matthias Egema, Miriam Elbrach, Madeleine D Harbiso, Irene Netchine, Luitgard Graul-neuma, Thomas EggermaAbstract:Abstract Background Maternal uniparental disomy (UPD) of chromosome 7 (upd(7)mat) accounts for approximately 10% of patients with Silver-Russell syndrome (SRS). For upd(7)mat and trisomy 7, a significant number of mechanisms have been proposed to explain the postzygotic formation of these chromosomal compositions, but all have been based on as small number of cases. To obtain the ratio of isodisomy and heterodisomy in UPDs (hUPD, iUPD) and to determine the underlying formation mechanisms, we analysed a large cohort of upd(7)mat patients (n = 73) by SNP Array typing. Based on these data, we discuss the UPDs and their underlying trisomy 7 formation mechanisms. Results A whole chromosome 7 maternal iUPD was confirmed in 28.8%, a mixture or complete maternal hUPD in 71.2% of patients. Conclusions We could demonstrate that nondisjunction mechanism affecting chromosome 7 are similar to that of the chromosomes more frequently involved in trisomy (and/or UPD), and that mechanisms other than trisomic rescue have a lower significance than previously suspected. Furthermore, we suggest SNP Array typing for future parent- and cell-stage-of origin studies in human aneuploidies as they allow the definite classification of trisomies and UPDs, and provide information on recombinational events and their suggested association with aneuploidy formation
Xiaofeng Zhou - One of the best experts on this subject based on the ideXlab platform.
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a forward backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high density single nucleotide polymorphism SNP Array
BMC Bioinformatics, 2007Co-Authors: Wei Sun, Zugen Chen, Sharoni Jacobs, Dione K Bailey, David T W Wong, Xiaofeng ZhouAbstract:Background DNA copy number aberration (CNA) is one of the key characteristics of cancer cells. Recent studies demonstrated the feasibility of utilizing high density single nucleotide polymorphism (SNP) genotyping Arrays to detect CNA. Compared with the two-color Array-based comparative genomic hybridization (Array-CGH), the SNP Arrays offer much higher probe density and lower signal-to-noise ratio at the single SNP level. To accurately identify small segments of CNA from SNP Array data, segmentation methods that are sensitive to CNA while resistant to noise are required.
