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Comparing variants related to chronic diseases from genome-wide association study (GWAS) and the cancer genome atlas (TCGA)
BackgroundSeveral genome-wide association studies (GWAS) have been performed to identify variants related to chronic diseases. Somatic variants in...
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Tissue of origin detection for cancer tumor using low-depth cfDNA samples through combination of tumor-specific methylation atlas and genome-wide methylation density in graph convolutional neural networks
BackgroundCell free DNA (cfDNA)-based assays hold great potential in detecting early cancer signals yet determining the tissue-of-origin (TOO) for...
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JCGA: the Japanese version of the Cancer Genome Atlas and its contribution to the interpretation of gene alterations detected in clinical cancer genome sequencing
With the emergence of next-generation sequencing (NGS)-based cancer gene panel tests in routine oncological practice in Japan, an easily...
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Pan-cancer atlas of somatic core and linker histone mutations
Recent genomic data points to a growing role for somatic mutations altering core histone and linker histone-encoding genes in cancer. However, the...
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An integrated tumor, immune and microbiome atlas of colon cancer
The lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome....
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The target atlas for antibody-drug conjugates across solid cancers
Antibody-Drug Conjugates (ADCs) represent a rapidly advancing category of oncology therapeutics, spanning the targeted therapy for both hematologic...
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Pan-cancer analysis of whole-genome doubling and its association with patient prognosis
BackgroundWhole-genome doubling (WGD) is a common mutation in cancer. Various studies have suggested that WGD is associated with a poor prognosis in...
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A single-cell atlas enables map** of homeostatic cellular shifts in the adult human breast
Here we use single-cell RNA sequencing to compile a human breast cell atlas assembled from 55 donors that had undergone reduction mammoplasties or...
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Integration of single-cell regulon atlas and multi-omics data for prognostic stratification and personalized treatment prediction in human lung adenocarcinoma
Transcriptional programs are often dysregulated in cancers. A comprehensive investigation of potential regulons is critical to the understanding of...
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Genetics of Cancer: Past, Present, and Future
Cancer is a disease of aberrant cells which evade the cell cycle checkpoints for proliferation and resists apoptotic signals. A cancer cell is...
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Single cell atlas of kidney cancer endothelial cells reveals distinct expression profiles and phenotypes
BackgroundTumor endothelial cells (TECs) represent the primary interface between the tumor microenvironment and circulating immune cells, however...
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PTEN-negative endometrial cancer cells protect their genome through enhanced DDB2 expression associated with augmented nucleotide excision repair
BackgroundEndometrial cancer (EC) arises from uterine endometrium tissue and is the most prevalent cancer of the female reproductive tract in...
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Genome-wide CRISPR screen identifies ESPL1 limits the response of gastric cancer cells to apatinib
Apatinib was the first anti-angiogenic agent approved for treatment of metastatic gastric cancer (GC). However, the emergence of resistance was...
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The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ
Microenvironmental and molecular factors mediating the progression of Breast Ductal Carcinoma In Situ (DCIS) are not well understood, impeding the...
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An integrated cell atlas of the lung in health and disease
Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and...
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Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants
The transferability and clinical value of genetic risk scores (GRSs) across populations remain limited due to an imbalance in genetic studies across...
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Single-molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer
Somatic mutations are a hallmark of tumorigenesis and may be useful for non-invasive diagnosis of cancer. We analyzed whole-genome sequencing data...
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Assessment of brain cancer atlas maps with multimodal imaging features
BackgroundGlioblastoma Multiforme (GBM) is a fast-growing and highly aggressive brain tumor that invades the nearby brain tissue and presents...
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The Human Genome and Its Variations
In this chapter, we will briefly describe the genetic adaption of anatomically modern humans due to migration from Africa to new geographic and...