BACKGROUND The full complement of DNA mutations that are responsible for the pathogenesis of acute myeloid leukemia (AML) is not yet known. METHODS We used massively parallel DNA sequencing to obtain a very high level of coverage (approximately 98%) of a primary, cytogenetically normal, de novo genome for AML with minimal maturation (AML-M1) and a matched normal skin genome. RESULTS We identified 12 acquired (somatic) mutations within the coding sequences of genes and 52 somatic point mutations in conserved or regulatory portions of the genome. All mutations appeared to be heterozygous and present in nearly all cells in the tumor sample. Four of the 64 mutations occurred in at least 1 additional AML sample in 188 samples that were tested. Mutations in NRAS and NPM1 had been identified previously in patients with AML, but two other mutations had not been identified. One of these mutations, in the IDH1 gene, was present in 15 of 187 additional AML genomes tested and was strongly associated with normal cytogenetic status; it was present in 13 of 80 cytogenetically normal samples (16%). The other was a nongenic mutation in a genomic region with regulatory potential and conservation in higher mammals; we detected it in one additional AML tumor. The AML genome that we sequenced contains approximately 750 point mutations, of which only a small fraction are likely to be relevant to pathogenesis. CONCLUSIONS By comparing the sequences of tumor and skin genomes of a patient with AML-M1, we have identified recurring mutations that may be relevant for pathogenesis.

Lay SummaryAcute myeloid leukemia is a highly malignant hematopoietic tumor that affects about 13,000 adults yearly in the United States. The treatment of this disease has changed little in the past two decades, since most of the genetic events that initiate the disease remain undiscovered. Whole genome sequencing is now possible at a reasonable cost and timeframe to utilize this approach for unbiased discovery of tumor-specific somatic mutations that alter the protein-coding genes. Here we show the results obtained by sequencing a typical acute myeloid leukemia genome and its matched normal counterpart, obtained from the patient’s skin. We discovered 10 genes with acquired mutations; two were previously described mutations thought to contribute to tumor progression, and 8 were novel mutations present in virtually all tumor cells at presentation and relapse, whose function is not yet known. Our study establishes whole genome sequencing as an unbiased method for discovering initiating mutations in cancer genomes, and for identifying novel genes that may respond to targeted therapies.We used massively parallel sequencing technology to sequence the genomic DNA of tumor and normal skin cells obtained from a patient with a typical presentation of FAB M1 Acute Myeloid Leukemia (AML) with normal cytogenetics. 32.7-fold ‘haploid’ coverage (98 billion bases) was obtained for the tumor genome, and 13.9-fold coverage (41.8 billion bases) was obtained for the normal sample. Of 2,647,695 well-supported Single Nucleotide Variants (SNVs) found in the tumor genome, 2,588,486 (97.7%) also were detected in the patient’s skin genome, limiting the number of variants that required further study. For the purposes of this initial study, we restricted our downstream analysis to the coding sequences of annotated genes: we found only eight heterozygous, non-synonymous somatic SNVs in the entire genome. All were novel, including mutations in protocadherin/cadherin family members (CDH24 and PCLKC), G-protein coupled receptors (GPR123 and EBI2), a protein phosphatase (PTPRT), a potential guanine nucleotide exchange factor (KNDC1), a peptide/drug transporter (SLC15A1), and a glutamate receptor gene (GRINL1B). We also detected previously described, recurrent somatic insertions in the FLT3 and NPM1 genes. Based on deep readcount data, we determined that all of these mutations (except FLT3) were present in nearly all tumor cells at presentation, and again at relapse 11 months later, suggesting that the patient had a single dominant clone containing all of the mutations. These results demonstrate the power of whole genome sequencing to discover novel cancer-associated mutations.

SUMMARY Analysis of molecular aberrations across multiple cancer types, known as pan-cancer analysis, identifies commonalities and differences in key biological processes dysregulated in cancer cells from diverse lineages. Pan-cancer analyses have been performed for adult1–4 but not pediatric cancers, which commonly occur in developing mesodermic rather than adult epithelial tissues5. Here we present a pan-cancer study of somatic alterations, including single nucleotide variants (SNVs), small insertion/deletions (indels), structural variations (SVs), copy number alterations (CNAs), gene fusions and internal tandem duplications (ITDs), in 1,699 pediatric leukemia and solid tumours across six histotypes, with whole-genome (WGS), whole-exome (WES) and transcriptome (RNA-seq) sequencing data processed under a uniform analytical framework (Online Methods and Extended Data Fig. 1). We report 142 driver genes in pediatric cancers, of which only 45% matched those found in adult pan-cancer studies and CNAs and SVs constituted the majority (62%) of events. Eleven genome-wide mutational signatures were identified, including one attributed to ultraviolet-light exposure in eight aneuploid leukemias. Transcription of the mutant allele was detectable for 34% of protein-coding mutations, and 20% exhibited allele-specific expression. These data provide a comprehensive genomic architecture for pediatric cancers and emphasize the need for pediatric cancer-specific development of precision therapies.

We present the molecular landscape of pediatric acute myeloid leukemia (AML) and characterize nearly 1,000 participants in Children’s Oncology Group (COG) AML trials. The COG–National Cancer Institute (NCI) TARGET AML initiative assessed cases by whole-genome, targeted DNA, mRNA and microRNA sequencing and CpG methylation profiling. Validated DNA variants corresponded to diverse, infrequent mutations, with fewer than 40 genes mutated in >2% of cases. In contrast, somatic structural variants, including new gene fusions and focal deletions of MBNL1, ZEB2 and ELF1, were disproportionately prevalent in young individuals as compared to adults. Conversely, mutations in DNMT3A and TP53, which were common in adults, were conspicuously absent from virtually all pediatric cases. New mutations in GATA2, FLT3 and CBL and recurrent mutations in MYC-ITD, NRAS, KRAS and WT1 were frequent in pediatric AML. Deletions, mutations and promoter DNA hypermethylation convergently impacted Wnt signaling, Polycomb repression, innate immune cell interactions and a cluster of zinc finger–encoding genes associated with KMT2A rearrangements. These results highlight the need for and facilitate the development of age-tailored targeted therapies for the treatment of pediatric AML.

However, the relevance of these findings to childhood AML remains unclear, since several of the most 53 common adult mutations appear far less prevalent in pediatric AML 6,7 . 54To date, no comprehensive characterization of pediatric AML has been described. Here, we report the 55 initial results of the TARGET (Therapeutically Applicable Research to Generate Effective Treatments) 56 AML initiative, a collaborative COG/NCI project to comprehensively characterize the mutational, 57 transcriptional, and epigenetic landscapes of a large, well-annotated cohort of pediatric AML. 58Comparing AML molecular profiles across age groups, we show that stark differences in mutations,d 59 structural variants and DNA methylation distinguish AML in infants, children, adolescents, and adults. 60 Results 61 Overview of cohort characteristics 62A total of 1023 children enrolled in COG studies are included in the TARGET AML dataset. 63Comprehensive clinical data, including clinical outcomes and test results for common sequence 64 aberrations (outlined in We carried out analyses of microRNA, mRNA, and/or DNA methylation in 412 subjects. A summary of 94 the assays performed and case-assay overlap is presented in Fig. S3. We compared our verified variants 95 to those of 177 adult AML cases from The Cancer Genome Atlas (TCGA) project 3 , stratified by the age 96 groupings outlined in Fig. 1a. The TARGET and TCGA discovery cohorts both contained numerous AYA 97 patients (Table S3). Importantly, our conclusions regarding the molecular characteristics of this age 98 group are identical when analyzing either or both cohorts (Fig. S4). 99 Somatic gene mutations in pediatric AML 100Like adult AML, pediatric AML has one of the lowest rates of mutation among molecularly well-101 characterized cancers (Fig. S5), with < 1 somatic, protein-coding change per megabase in most cases. 102However, the landscape of somatic variants in pediatric AML is markedly different from that reported in 103 adults 3,4 (Figs. 2b, S6-S7, Table S4). RAS, KIT, and FLT3 alterations, including novel, pediatric-specific 104 FLT3 mutations (FLT3.N), are more common in children. Mutational burden increases with age, yet older 105 patients have relatively fewer recurrent cytogenetic alterations. Indeed, the number of coding SNVs, 106 within and across cohorts, is best predicted by age (Fig. 2c, p<10 -15 ) and by cytogenetic subgroup. In 107 contradistinction to the higher prevalence of small sequence variants in older patients, recurrent 108 structural alterations, fusions, and focal copy number aberrations are more common in younger patients 109 (Figs. 2d-e, p<10 -3 , see below). Patients with CBFA2T3-GLIS2, KMT2A, or NUP98 fusions tend to have 110 . CC-BY 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/125609 doi: bioRxiv preprint first posted online Jun. 13, 2017; fewer mutations (p<10 -9 ), with subgroups demonstrating inferior clinical outcome...

Activating mutations in tyrosine kinase (TK) genes (eg, FLT3 and KIT) are found in more than 30% of patients with de novo acute myeloid leukemia (AML); many groups have speculated that mutations in other TK genes may be present in the remaining 70%. We performed highthroughput resequencing of the kinase domains of 26 TK genes (11 receptor TK; 15 cytoplasmic TK) expressed in most AML patients using genomic DNA from the bone marrow (tumor) and matched skin biopsy samples ("germline") from 94 patients with de novo AML; sequence variants were validated in an additional 94 AML tumor samples (14.3 million base pairs of sequence were obtained and analyzed). We identified known somatic mutations in FLT3, KIT, and JAK2 TK genes at the expected frequencies and found 4 novel somatic mutations, JAK1 V623A , JAK1 T478S , DDR1 A803V , and NTRK1 S677N , once each in 4 respective patients of 188 tested. We also identified novel germline sequence changes encoding amino acid substitutions (ie, nonsynonymous changes) in 14 TK genes, including TYK2, which had the largest number of nonsynonymous sequence variants (11 total detected). Additional studies will be required to define the roles that these somatic and germline TK gene variants play in AML pathogenesis. (Blood. 2008; 111:4797-4808)

Cytogenetic analysis of acute myeloid leukemia (AML) cells has accelerated the identification of genes important for AML pathogenesis. To complement cytogenetic studies and to identify genes altered in AML genomes, we performed genome-wide copy number analysis with paired normal and tumor DNA obtained from 86 adult patients with de novo AML using 1.85 million feature SNP arrays. Acquired copy number alterations (CNAs) were confirmed using an ultra-dense array comparative genomic hybridization platform. A total of 201 somatic CNAs were found in the 86 AML genomes (mean, 2.34 CNAs per genome), with French-AmericanBritish system M6 and M7 genomes containing the most changes (10 -29 CNAs per genome). Twenty-four percent of AML patients with normal cytogenetics had CNA, whereas 40% of patients with an abnormal karyotype had additional CNA detected by SNP array, and several CNA regions were recurrent. The mRNA expression levels of 57 genes were significantly altered in 27 of 50 recurrent CNA regions <5 megabases in size. A total of 8 uniparental disomy (UPD) segments were identified in the 86 genomes; 6 of 8 UPD calls occurred in samples with a normal karyotype. Collectively, 34 of 86 AML genomes (40%) contained alterations not found with cytogenetics, and 98% of these regions contained genes. Of 86 genomes, 43 (50%) had no CNA or UPD at this level of resolution. In this study of 86 adult AML genomes, the use of an unbiased high-resolution genomic screen identified many genes not previously implicated in AML that may be relevant for pathogenesis, along with many known oncogenes and tumor suppressor genes. AML ͉ array CGH ͉ genomics ͉ SNP arrayA cute myeloid leukemia (AML) is a heterogeneous group of diseases currently classified by abnormalities in bone marrow morphology, karyotype, acquired gene mutations, and alterations in gene expression (1-3). Although the identification of specific gene mutations has resulted in improved treatments and outcomes for some AML patients (4), enormous clinical heterogeneity exists and may reflect the presence of as-yet undetected initiating and cooperating mutations. Therefore, the discovery of somatic mutations in the genomes of AML patients with normal and abnormal karyotypes will advance our understanding of the genetics underlying AML and should lead to more specific therapies and better patient classification schemes.The discovery of previously uncharacterized genes mutated in acute lymphoblastic leukemia (ALL) was recently reported using SNP array technology for DNA copy number analysis (5). SNP array platforms can detect genomic amplifications, deletions, SNP loss of heterozygosity (LOH), and regions of uniparental disomy (UPD) (copy-neutral LOH events) in cancer cells. Early studies using SNP arrays and array comparative genomic hybridization (CGH) platforms have suggested that both copy number alterations (CNAs) and UPD are common in AML genomes (6-12). However, these studies used low-resolution arrays, often used reference DNA that was not obtained from the same patient's n...

The genomic and clinical information used to develop and implement therapeutic approaches for AML originated primarily from adult patients and has been generalized to patients with pediatric AML. However, age-specific molecular alterations are becoming more evident and may signify the need to age-stratify treatment regimens. The NCI/COG TARGET-AML initiative employed whole exome capture sequencing (WXS) to interrogate the genomic landscape of matched trios representing specimens collected upon diagnosis, remission, and relapse from 20 cases of de novo childhood AML. One hundred forty-five somatic variants at diagnosis (median 6 mutations per patient) and 149 variants at relapse (median 6.5 mutations) were identified and verified by orthogonal methodologies. Recurrent somatic variants (in {greater than or equal to}2 patients) were identified for 10 genes (FLT3, NRAS, PTPN11, WT1, TET2, DHX15, DHX30, KIT, ETV6, KRAS), with variable persistence at relapse. The variant allele fraction (VAF), used to measure the prevalence of somatic mutations, varied widely at diagnosis. Mutations that persisted from diagnosis to relapse had a significantly higher diagnostic VAF compared to those that resolved at relapse (median VAF 0.43 vs. 0.24, P<0.001). Further analysis revealed that 90% of the diagnostic variants with VAF >0.4 persisted to relapse compared to 28% with VAF <0.2 (P<0.001). This study demonstrates significant variability in the mutational profile and clonal evolution of pediatric AML from diagnosis to relapse. Furthermore, mutations with high VAF at diagnosis, representing variants shared across a leukemic clonal structure, may constrain the genomic landscape at relapse and help to define key pathways for therapeutic targeting.