Assume gains and losses of single or multiple copy numbers can happen with equal probability for a genome region. One consequence of these assumptions is that the chance of observing aberration events that happen at different time points sharing the same breakpoint is very slim. Another consequence is that all aberrant segments, irrespective of their spans and copy numbers, are equally important and should contribute as such to the estimation of CINGEC index. The CINGEC algorithm proceeds from a copy number sequence of a chromosome s = (s [1], …, s[n]), (s[i] M -p, …, q; p, q .0; s[i] ? s[i+1]) obtained after discretizing aCGH data into copy number levels (CNLs) using segmentation (Figure 1). Here, positive and negative values represent different levels of gains and losses, respectively. Obviously, copy number sequence is composed of aberrant subsequences delimited by normal copy number segments (CNL = 0). In CINGEC, the number of aberration events of a chromosome is estimated by the sum of aberration events from aberrant subsequences. The number of aberration events of an aberrant subsequence increases by 1 if CNL transits into a new one (s[i] 1 s[j] (j,i)) or CNL transitsinto earlier than the immediate previous level (s[i] = s[m], m,i-1). The Title Loaded From File latter criterion is based on the observation that the chance of two or 16985061 more boundaries of independent aberration events coinciding with each other is very slim and it is more natural to assume an intervention of another aberration event that forces different breakpoints align with each other. If CNL returns to any of its previous levels, all intermediate CNLs between the departing and returning events will be expunged and estimation moves to next CNL. Final CINGEC estimate is the sum of all aberration events in autosomal chromosomes to avoid complications from sex chromosomes. Algorithmic details with an illustrative example are described in Method S1.Gene Expression Signature (CINGECS) ConstructionAgilent 244K chip aCGH data of 254 MM patients from Multiple Myeloma Research Consortium (MMRC) reference collection were downloaded from Gene Expression Omnibus (GEO; GSE26849). [7] We segmented the aCGH data by using the CBS algorithm [11] Title Loaded From File implemented in `DNACopy’ R library [12] using default parameters and CINGEC values were estimated. MAS5 preprocessed Affymetrix HG-U133 Plus 2.0 GEP data for 304 MM patients from MMRC reference collection were downloaded from GEO (GSE26760). 246 of the MMRC samples had both aCGH and GEP data. We split CINGEC values of these samples into 4 quartiles and the differential gene expression between top and bottom quartile CIN groups was examined using the SAM algorithm [13] implemented in `siggenes’ R library [14]. Probesets with p-values #0.001 and false discovery rate (fdr) #0.05 and at least 2-fold expression difference between the top and bottom CIN groups were selected as CINGECS, the CINGEC-associated GEP signature.Chromosome Instability and Prognosis in MMFigure 2. OS difference among different inter-quartile groups by (a) CINGEC, (b) GII of Mayo patient aCGH data and (c) CINGEC, (d) GII of UAMS patient. doi:10.1371/journal.pone.0066361.gPathway Analysis of CINGECSIn order to identify biological pathways enriched by member genes of CINGECS, we utilized impact factor (IF) analysis [15] implemented in Onto-Tools. [16] Contrary to many pathwaybased analysis algorithms that consider only the enrichment of gene lists within specific pathways, IF analysis puts.Assume gains and losses of single or multiple copy numbers can happen with equal probability for a genome region. One consequence of these assumptions is that the chance of observing aberration events that happen at different time points sharing the same breakpoint is very slim. Another consequence is that all aberrant segments, irrespective of their spans and copy numbers, are equally important and should contribute as such to the estimation of CINGEC index. The CINGEC algorithm proceeds from a copy number sequence of a chromosome s = (s [1], …, s[n]), (s[i] M -p, …, q; p, q .0; s[i] ? s[i+1]) obtained after discretizing aCGH data into copy number levels (CNLs) using segmentation (Figure 1). Here, positive and negative values represent different levels of gains and losses, respectively. Obviously, copy number sequence is composed of aberrant subsequences delimited by normal copy number segments (CNL = 0). In CINGEC, the number of aberration events of a chromosome is estimated by the sum of aberration events from aberrant subsequences. The number of aberration events of an aberrant subsequence increases by 1 if CNL transits into a new one (s[i] 1 s[j] (j,i)) or CNL transitsinto earlier than the immediate previous level (s[i] = s[m], m,i-1). The latter criterion is based on the observation that the chance of two or 16985061 more boundaries of independent aberration events coinciding with each other is very slim and it is more natural to assume an intervention of another aberration event that forces different breakpoints align with each other. If CNL returns to any of its previous levels, all intermediate CNLs between the departing and returning events will be expunged and estimation moves to next CNL. Final CINGEC estimate is the sum of all aberration events in autosomal chromosomes to avoid complications from sex chromosomes. Algorithmic details with an illustrative example are described in Method S1.Gene Expression Signature (CINGECS) ConstructionAgilent 244K chip aCGH data of 254 MM patients from Multiple Myeloma Research Consortium (MMRC) reference collection were downloaded from Gene Expression Omnibus (GEO; GSE26849). [7] We segmented the aCGH data by using the CBS algorithm [11] implemented in `DNACopy’ R library [12] using default parameters and CINGEC values were estimated. MAS5 preprocessed Affymetrix HG-U133 Plus 2.0 GEP data for 304 MM patients from MMRC reference collection were downloaded from GEO (GSE26760). 246 of the MMRC samples had both aCGH and GEP data. We split CINGEC values of these samples into 4 quartiles and the differential gene expression between top and bottom quartile CIN groups was examined using the SAM algorithm [13] implemented in `siggenes’ R library [14]. Probesets with p-values #0.001 and false discovery rate (fdr) #0.05 and at least 2-fold expression difference between the top and bottom CIN groups were selected as CINGECS, the CINGEC-associated GEP signature.Chromosome Instability and Prognosis in MMFigure 2. OS difference among different inter-quartile groups by (a) CINGEC, (b) GII of Mayo patient aCGH data and (c) CINGEC, (d) GII of UAMS patient. doi:10.1371/journal.pone.0066361.gPathway Analysis of CINGECSIn order to identify biological pathways enriched by member genes of CINGECS, we utilized impact factor (IF) analysis [15] implemented in Onto-Tools. [16] Contrary to many pathwaybased analysis algorithms that consider only the enrichment of gene lists within specific pathways, IF analysis puts.
