TITLES AND LEGENDS TO SUPPLEMENRATY FIGURES
Supplementary Table 1. Primers pairs for direct sequencing of high heterozygous SNP
mapping within the region of UPD.
All SNPs are Affy 100K except rs226981 (* Illumina HumanMap300 BeadChip). For each SNP is
reported the chromosome, cytoband, physical position, allele, heterozygous frequency and
forward/reverse primer used for direct sequencing.
Supplementary Table 2. Complete list of aberrations.
Numbers were calculated as the higher value of LOH probability, or the average CN value within
the affected region for UPD and CNA, respectively, if present in the correspondent sample at
diagnosis (DX), remission (REM), and relapse (REL). A selection of relevant genes related to
human tumors mapping within the altered regions is listed. The extent of overlap with Lencz’s ROH
(ref. 23) is reported: # extensive overlap (>25%); ¤ partial overlap (10-25%); § slight overlap
(<10%). For overlapping UPD, the ROH ID from Lencz et al (ref. 23) and the maximum extent (%)
of overlap is indicated. * confirmed with CNAG; n.a. sample not available for analysis.
Supplementary Table 3. List of UPD regions found at diagnosis.
List of 98 segmental chromosomal regions in which at least one event on UPD was detected at
diagnosis. For each region is reported the correspondent physical position (chromosome, cytoband,
start, end), length (Kb), the number of SNPs contained (#SNPs) and the percentage of samples
harbouring the aberration (% Sample) among the 46 samples (28 diagnoses +18 remissions)
displayed in Supplementary Fig.2. For the two cases indicated with asterisk (*) the median LOH
probability is slightly lower than the threshold value (P<0.5).
Supplementary Table 4. List of genes mapping within the region of UPD found at diagnosis.
The complete list of Genes (n=2141) mapping within the 98 UPD regions found at diagnosis (listed
in Supplementary Table 3), with details of chromosomal position, start, end, gene product and
entrez ID, was obtained by using UCSC Genome Browser database.
Supplementary Table 5. List of genes within the recurrent UPD regions.
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The complete list of Genes (n=187) mapping within the 20 regions of recurrent UPD found at
diagnoses (listed in Table 3), with details of chromosomal position, start, end, gene product and
entrez ID, was obtained by using UCSC Genome Browser database.
Supplementary Figure 1. Example of CNA and UPD in a representative chromosome.
Example of CN and LOH analysis performed by dChip on chromosome 7. Black arrows represent
segmental CN-neutral LOH regions (i.e. UPD(7)(q21.11) in pt.2 at REL, UPD(7)(q21.3q32.3) in
pt.9 at DX, REM and REL, UPD(7)(q31.33q32.1) in pt.11 at DX and REL), green arrows represent
CN loss (i.e. del(7p) in pt.9 and 22 at REL, del(7)(q11.21) in pt.14 at DX) and red arrows represent
CN gain (i.e. amp(7q) in pt.21 and 22 at REL). Pt.21 and 22 display an Iso(7q) at REL.
Supplementary Figure 2. Regional LOH analysis.
Graphic visualization of LOH analysis performed by dChip on Infant ALL diagnostic samples
(n=28) paired with their corresponding remission (n=18), when available. The plot shows a selection
of chromosomal regions in which at least one event of LOH with CN neutral (segmental UPD)
occurred among the diagnoses. Rows represent chromosome regions and columns represent samples.
Paired diagnosis (DX) and remission (REM) are indicated for each patient. Based on SNP data 98
chromosome regions were found (on the left), containing 15054 SNP markers. The LOH probability
is displayed ranging from blue (1) to white (0.5) to yellow (0).
Supplementary Figure 3. UPD(14)(q21.2).
A: SNP 100K calls of 4 Infant ALL patients (pt.3,4,8 and 21) compared with 6 normal infants
(CNTRL1-6). DX: diagnosis; REM: remission; REL: relapse. SNP physical position deriving from
GTYPE raw data refers to hg18 annotation B: Numbers indicates the higher probability of LOH
within the region among the affected patients in their corresponding samples at DX, REM and REL.
The samples indicated with asterisk (*) were detected exclusively with CNAG software. n.a. samples
not available C: The segmental UPD was confirmed with CNAG (one representative case is shown)
D: The homozygous status of 4 SNPs (labelled in red in panel A) with high heterozygous frequency
in the 4 Infant ALL cases was validated by sequencing.
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Supplementary Figure 4. UPD(7)(q31.22q32.1).
A: SNP 100K calls of 3 Infant ALL patients (pt.1,9 and 11) compared with 6 normal infants
(CNTRL1-6). DX: diagnosis; REM: remission; REL: relapse. SNP physical position deriving from
GTYPE raw data refers to hg18 annotation. B: Numbers indicates the higher probability of LOH
within the region among the affected patients in their corresponding samples at DX, REM and REL.
n.a. samples not available C: The segmental UPD was confirmed with CNAG (all the three cases are
shown). The red box indicates the minimal common region. D: The homozygous status of 4 SNPs
(labelled in red in panel A) with high heterozygous frequency in the 3 Infant ALL cases was
validated by sequencing.
Supplementary Figure 5. UPD(8)(q21.13).
A: SNP 100K calls of 2 Infant ALL patients (pt.19 and 21) compared with 6 normal controls
(CNTRL1-6). DX: diagnosis; REM: remission; REL: relapse. SNP physical position deriving from
GTYPE raw data refers to hg18 annotation. B: Numbers indicates the higher probability of LOH
within the region among the affected patients in their corresponding samples at DX, REM and REL.
n.a. samples not available C: The segmental UPD was confirmed with CNAG (one representative
case is shown) D: The homozygous status of 4 SNPs (labelled in red in panel A) with high
heterozygous frequency in the 2 Infant ALL cases was validated by sequencing.
Supplementary Figure 6. UPD(8)(q24.11).
A: SNP 100K calls of 2 Infant ALL patients (pt.2 and 9) compared with 6 normal controls
(CNTRL1-6). DX: diagnosis; REM: remission; REL: relapse. SNP physical position deriving from
GTYPE raw data refers to hg18 annotation. B: Numbers indicates the higher probability of LOH
within the region among the affected patients in their corresponding samples at DX, REM and REL.
n.a. samples not available C: The segmental UPD was confirmed with CNAG (both cases are
shown). The red box indicate the minimal common region. D: The homozygous status of 4 SNPs
(labelled in red in panel A) with high heterozygous frequency in the 2 Infant ALL cases was
validated by sequencing.
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