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Article
Open AccessMutation-Attention (MuAt): deep representation learning of somatic mutations for tumour ty** and subty**
Cancer genome sequencing enables accurate classification of tumours and tumour subtypes. However, prediction performance is still limited using exome-only sequencing and for tumour types with low somatic mutat...
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Article
Open AccessIdentification of multiplicatively acting modulatory mutational signatures in cancer
A deep understanding of carcinogenesis at the DNA level underpins many advances in cancer prevention and treatment. Mutational signatures provide a breakthrough conceptualisation, as well as an analysis framew...
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Article
Open AccessEnrichment of cancer-predisposing germline variants in adult and pediatric patients with acute lymphoblastic leukemia
Despite recent progress in acute lymphoblastic leukemia (ALL) therapies, a significant subset of adult and pediatric ALL patients has a dismal prognosis. Better understanding of leukemogenesis and recognition ...
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Article
Open AccesssPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies
Meta-analysis has been established as an effective approach to combining summary statistics of several genome-wide association studies (GWAS). However, the accuracy of meta-analysis can be attenuated in the pr...
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Article
Open AccessRetrotransposon insertions can initiate colorectal cancer and are associated with poor survival
Genomic instability pathways in colorectal cancer (CRC) have been extensively studied, but the role of retrotransposition in colorectal carcinogenesis remains poorly understood. Although retrotransposons are u...
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Article
Open AccessExome and immune cell score analyses reveal great variation within synchronous primary colorectal cancers
Approximately 4% of colorectal cancer (CRC) patients have at least two simultaneous cancers in the colon. Due to the shared environment, these synchronous CRCs (SCRCs) provide a unique setting to study colorec...
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Article
Discovery of potential causative mutations in human coding and noncoding genome with the interactive software BasePlayer
Next-generation sequencing (NGS) is routinely applied in life sciences and clinical practice, but interpretation of the massive quantities of genomic data produced has become a critical challenge. The genome-w...
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Article
Germline alterations in a consecutive series of acute myeloid leukemia
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Article
Open AccessContribution of allelic imbalance to colorectal cancer
Point mutations in cancer have been extensively studied but chromosomal gains and losses have been more challenging to interpret due to their unspecific nature. Here we examine high-resolution allelic imbalanc...
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Article
Open AccessTowards pan-genome read alignment to improve variation calling
Typical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exom...
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Article
Open AccessGlobal metabolomic profiling of uterine leiomyomas
Uterine leiomyomas can be classified into molecularly distinct subtypes according to their genetic triggers: MED12 mutations, HMGA2 upregulation, or inactivation of FH. The aim of this study was to identify metab...
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Article
Open AccessDetection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing
Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy...
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Article
Open AccessMultiple clinical characteristics separate MED12-mutation-positive and -negative uterine leiomyomas
Up to 86% of uterine leiomyomas harbour somatic mutations in mediator complex subunit 12 (MED12). These mutations have been associated with conventional histology, smaller tumour size, and larger number of tumour...
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Article
Open AccessWhole-exome sequencing identifies novel candidate predisposition genes for familial polycythemia vera
Polycythemia vera (PV), characterized by massive production of erythrocytes, is one of the myeloproliferative neoplasms. Most patients carry a somatic gain-of-function mutation in JAK2, c.1849G > T (p.Val617Phe),...
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Article
Open AccessWhole-genome metabolic model of Trichoderma reesei built by comparative reconstruction
Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of ...
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Article
Open AccessMED12 mutations and FH inactivation are mutually exclusive in uterine leiomyomas
Uterine leiomyomas from hereditary leiomyomatosis and renal cell cancer (HLRCC) patients are driven by fumarate hydratase (FH) inactivation or occasionally by mediator complex subunit 12 (MED12) mutations. The ai...
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Article
3′-UTR poly(T/U) repeat of EWSR1 is altered in microsatellite unstable colorectal cancer with nearly perfect sensitivity
Approximately 15 % of colorectal cancers exhibit instability of short nucleotide repeat regions, microsatellites. These tumors display a unique clinicopathologic profile and the microsatellite instability stat...
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Article
CTCF/cohesin-binding sites are frequently mutated in cancer
Lauri Aaltonen, Jussi Taipale and colleagues report frequent mutation of CTCF- and cohesin-binding sites (CBSs) in multiple cancer types. They find that the frequency of CBS mutations in microsatellite-stable ...
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Article
Open AccessThe Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanv...
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Chapter and Conference Paper
Reconstructing Gapless Ancestral Metabolic Networks
We present a method for inferring the structure of ancestral metabolic networks directly from the networks of observed species and their phylogenetic tree. In particular, we aim to minimize the number of mutat...
