METHODS
Patient samples
DNA samples for whole exome sequencing (WES) were obtained from normal
tissue (oral mucosa) and tumor BM. The study was approved by the ethical research
and animal care committee from the Institute of Health Carlos III (CEI PI 32_2009).
DNA was extracted by the phenol–chloroform method and the quality and quantity of
purified DNA was assessed by fluorometry (Qubit, Invitrogen) and gel electrophoresis.
WES and bioinformatic analysis
The preparation of shotgun libraries from the leukemic and non-leukemic
genomic DNA followed the “SureSelect Human All Exon Kit” protocol (Agilent
Technologies, Santa Clara, CA), covering 50 Mb of coding exons (approximately 1.60%
of the genome). One to three µg of high molecular weight genomic DNA from each
sample was fragmented by acoustic shearing on a Covaris S2 instrument. Fractions of
150–300 bp were ligated to Illumina adapters and PCR-amplified for 6 cycles. For exon
enrichment, 300 ng of library were hybridized to SureSelect Human All Exon Capture
kit for 24 h at 65ºC. Biotinylated hybrids were captured, and the enriched libraries
were completed by amplifying with 12 cycles of PCR. The resulting purified DNA library
was applied to an Illumina flow cell for cluster generation and sequenced using the
Illumina Genome Analyzer IIx generating 2x76 base pair, paired-end reads by following
the manufacturer protocols.
Exome variant analysis and biological impact predictions were performed by
RUbioSeq software (1) using default parameters for somatic variation analysis. In
detail, sequencing data were first checked by FastQC for quality control checks on raw
sequence data and then aligned to the human reference genome (GRCh37) using
Burrows-Wheeler alignment (BWA) (2). That reads unmapped by BWA were realigned
using BFAST (3). Somatic variants were identified using the Unified Genotyper v2
available at the GATK (4). For variant calling we used GATK Unified Genotyper v2
applying the ‘‘Discovery’’ genotyping mode and default parameters for filtering. Thus,
SNPs available at dbSNP 132 (hg19) and those reported by the 1000 Genomes Project,
as well as changes present in the matched normal DNA and silent changes, were
filtered out from VCF output files (5). The GATK QUAL field was employed for ranking
selected somatic variants. Biological impact predictions for detected variants were
obtained from Ensembl Variant Effect Predictor (6). In order to estimate the damaging
character of the missense mutations, we used two different algorithms: SIFT and
PolyPhen-2. A workflow of WES and the bioinformatic analysis is provide in
Supplementary Figure 3.
We used targeted re-sequencing to validate candidate variants. Ion
semiconductor sequencing on the Ion Torrent PGM® was performed using the
HaloPlex target enrichment system (Agilent). Briefly, patients DNAs were digested by a
cocktail of restriction enzymes and hybridized to specific probes incorporating Ion
Torrent specific sequences motifs. Hybridized molecules were captured with magnetic
beads, amplified using indexed primers, template onto Ion Sphere Particles (Ion One
Touch 200 Template Kit v2 DL), and, finally, sequenced with the Ion PGM Sequencing
200 Kit on an Ion 316 chip. Data were analyzed with Variant Caller v2.2.3-31149 using
default parameters (all Life Technologies, Carlsbad, CA).
Whole-transcriptome Sequencing and bioinformatics analyses
Total RNA was extracted from BM leukemia cells and from CD34+ cells (normal
control) by TRIzol (Life Technologies, Carlsbad, CA), following the manufacturers
protocol; 250-1000 ng of total RNA were used for the synthesis of cDNA libraries with
TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA) according to the
manufacturers recommendations. Sequencing by synthesis was performed on
HiScanSQ sequencer (Illumina) at 75bp in paired end. Sequenced reads were qualitychecked with FastQC. The 75-nt paired-end reads were aligned to the human genome
(GRCh37/hg19) with TopHat-2.0.4 (7) (using Bowtie 0.12.7 (8) and Samtools 0.1.16 (9)),
allowing two mismatches and five multihits. Fusion transcripts were obtained with
TopHat-Fusion (10). Transcripts differential expression between samples was
calculated with Cuffdiff (Cufflinks 1.3.0 (7)), using the human genome annotation data
set Homo_sapiens.GRCh37.65 from Ensembl. LUC7L2 expression was validate by
quantitative real-time RT-PCR starting from total RNA from the patient sample, which
was reverse-transcribed using random hexamer primers with the TaqMan® Gold RT-
PCR Kit (Hs00255388_m1 - Applied Biosystems, Foster City, CA). The Calibrated
Normalized Relative Quantity, taking into account target- and run-specific
amplification efficiencies, was calculated using endogenous GAPDH expression with
the Qbase software application. PIM3-SCO2 fusion transcripts were amplified (PIM32F: CGCGACATTAAGGACGAAAA / SCO2-2R: GCCCTGCCTTGACAAAAG) and sequenced
with BigDye terminator v3.1 Cycle Sequencing kit (PE Applied Biosystems, Foster City,
CA) on an Applied Biosystems 310 analyzer.
Ingenuity Pathway Ananlysis
Genes found to be mutated among the cases were subjected to Ingenuity
Pathways Analysis (IPA) (Ingenuity Systems) and used as a starting point for building
biological networks (http://www.ingenuity.com/products/ipa). IPA uses the proteins
from the highest-scoring network to extract a connectivity pathway that relates
candidate proteins to each other based on their interactions.
Supplementary Figure 1: Integrative Genome Viewer image from RNA-seq data. We
found an altered pattern of splicing in the mRNA species transcribed from the RUNX1
gene. At the 3’ splice site of RUNX1 intron 5, the un-spliced reads were almost 3 times
more frequent in the mutated patient than the normal control.
Supplementary Figure 2: Functional classification of genes differently expressed
between CNL cells and normal control (CD34+), according to IPA, revealed an
enrichment of categories like cell signaling; cell death and survival; and gene
expression (B-H p-value <0.05).
Supplementary Figure 3: Sequencing workflow and bioinformatics pipeline for
identification of somatic mutations. After alignment of the sequencing reads from
DNA samples of CNL and normal cells to the human reference genome, a series of
filters were applied to discard reads that were not usable for the downstream purpose
of somatic mutation discovery. Sequence variants fulfilling the additional criteria were
subjected to Sanger sequencing validation.
Supplementary Figure 4: Sanger sequencing
(c.C79T/p.R93*) mutation in the CNL patient.
chromatograms
of
LUC7L2
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