An Algorithm for Bounding Error in Estimates of Genome Copy Number Variations Using SNP Array Technology

Noise strongly affects measurements of chromosomal changes provided using the modern single nucleotide polymorphism (SNP) array technology. This makes difficulties in the estimation of genome copy number variations (CNVs) essential for human life. We propose an efficient algorithm for computing the confidence upper and lower boundary limits in order to guarantee an existence of genomic changes with a required probability. The algorithm is designed to approximate the breakpoint jitter probability with the discrete skew Laplace distribution. We test some SNP-based measurements by the upper and lower confidence bound masks and show special cases when the estimated chromosomal change may not exist and the breakpoint locations cannot be estimated with sufficient accuracy.

[1]  J. Bonfield,et al.  Finishing the euchromatic sequence of the human genome , 2004, Nature.

[2]  International Human Genome Sequencing Consortium.  Finishing the euchromatic sequence of the human genome , 2004 .

[3]  E. Barillot,et al.  Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays , 2009, Genome Biology.

[4]  J. Sebat,et al.  Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. , 2003, Genome research.

[5]  Yuriy S. Shmaliy,et al.  Jitter probability in the breakpoints of discrete sparse piecewise-constant signals , 2013, 21st European Signal Processing Conference (EUSIPCO 2013).

[6]  Yuriy S. Shmaliy,et al.  Confidence limits for genome DNA copy number variations in HR-CGH array measurements , 2014, Biomed. Signal Process. Control..

[7]  Richard A. Firtel,et al.  Organization of the ribosomal RNA genes of dictyostelium discoideum: Mapping of the nontrascribed spacer regions , 1976, Cell.

[8]  E. Barillot,et al.  Analysis of Somatic Alterations in Cancer Genome: From SNP Arrays to Next Generation Sequencing , 2013 .

[9]  Tomasz J. Kozubowski,et al.  A Skew Laplace Distribution on Integers , 2006 .

[10]  Yuriy S. Shmaliy,et al.  Time-variant forward-backward FIR denoising of piecewise-smooth signals , 2013 .

[11]  M. Stern,et al.  Genomic Signature of Homologous Recombination Deficiency in Breast and Ovarian Cancers , 2013 .

[12]  J. Landers,et al.  Using high-throughput SNP technologies to study cancer , 2006, Oncogene.

[13]  M. Wigler,et al.  Circular binary segmentation for the analysis of array-based DNA copy number data. , 2004, Biostatistics.

[14]  Yuriy S. Shmaliy,et al.  Confidence masks for genome DNA copy number variations in applications to HR-CGH array measurements , 2014, Biomed. Signal Process. Control..

[15]  E. S. Venkatraman,et al.  A faster circular binary segmentation algorithm for the analysis of array CGH data , 2007, Bioinform..

[16]  Ahmed H. Tewfik,et al.  Detecting Changes in DNA Copy Number: Reviewing signal processing techniques , 2012, IEEE Signal Processing Magazine.

[17]  P. Stankiewicz,et al.  Structural variation in the human genome and its role in disease. , 2010, Annual review of medicine.