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These mutations often confer a large effect on the development of a disease, but are rare in the population.

These variants are common in the population, but have a smaller effect on disease development.

The concept of genetic variants having different frequencies and effect sizes is molded by natural selection.

Genetic studies where researchers look for common genetic variants associated with a disease. They do this by comparing the genomes of people with the disease to those without.

A significant challenge in GWAS studies where a large portion of the genetic variation associated with a disease remains unexplained.

The field of study that focuses on understanding the genetic alterations that occur within cancer cells.

Genetic changes acquired during a person's lifetime, primarily drive the development of cancer.

Genes that increase the risk of developing cancer when a person inherits a mutation in them.

Genes that protect cells from uncontrolled growth. When both copies of a tumor suppressor gene are inactivated, cells can grow uncontrollably.

Genes that promote cell growth and division. When these genes are mutated or overactive, they can contribute to cancer.

This hypothesis explains how tumor suppressor genes are inactivated in cancer. It involves two steps: an initial mutation in one copy of the gene followed by a second mutation or loss of the remaining copy.

Sequencing errors, differences between the individual's genome and the reference genome, and the repetitive nature of the genome pose challenges for accurate mapping.

The process of predicting the DNA sequence from images generated by a sequencing device.

Paired reads are DNA fragments that originate from the same DNA molecule but are sequenced from opposite ends. This helps to improve the accuracy of mapping reads to the reference genome.

A reference genome is a standard DNA sequence that is used as a basis for comparing and analyzing individual genomes.

The process of aligning sequenced DNA fragments (reads) to a reference genome. This allows for the identification of variations in the individual's genome compared to the reference.

Short RNA molecules (24-30 nucleotides) primarily found in germline cells. They bind to PIWI proteins and regulate chromatin structure, influencing gene expression.

Long non-coding RNAs are linear RNA molecules exceeding 200 nucleotides. They interact with DNA, RNA, and proteins, influencing gene expression and cellular processes.

Circular RNAs are circular or ring-like RNA molecules greater than 200 nucleotides. They interact with proteins, influencing gene expression and cellular processes.

Non-coding RNAs (ncRNAs) play a key role in regulating gene expression in cancer. They can influence transcription, post-transcriptional processes, and epigenetic modifications.

miRNAs like miR-21 can promote uncontrolled cell growth, driving cancer cell proliferation.

ncRNAs like MALAT1 can suppress apoptosis, allowing cancer cells to evade programmed cell death, contributing to cancer survival.

ncRNAs like HOTAIR can contribute to metastasis by regulating epithelial-mesenchymal transition (EMT), allowing cells to spread and invade other tissues.

Non-coding RNAs can be detected in blood, urine, and other body fluids. Cancer-specific patterns of ncRNAs can serve as non-invasive biomarkers for early detection.

Variants detected in a tumor sample may not be true somatic mutations, as they may be present in the matching germline DNA with a frequency of 1 in 1000 bases.

Sequencing depth refers to the number of times a specific region of DNA is sequenced. A higher sequencing depth is essential to detect low-frequency variants with high confidence and minimize false-positive results.

Sequencing and sequencer errors can introduce artifacts into the sequencing data, leading to false variant calls. These errors contribute to the limitations of mutation detection sensitivity.

Read pairs derived from the same DNA fragment are expected to have one read on the forward strand and the other on the reverse strand. This orientation provides information about the fragment size and helps identify structural variations.

Discordant read pairs are those where the reads from a fragment do not align according to the expected orientation and distance, suggesting a structural variation in the DNA.

A structural variant (SV) is a change in the arrangement of DNA segments beyond single nucleotide polymorphisms (SNPs). It can involve insertions, deletions, inversions, duplications, and complex rearrangements of the DNA.

The VCF (Variant Call Format) is a standardized format for storing and exchanging genomic variant information. It uses tab-delimited fields to define variant types, positions, and other relevant details.

Non-coding RNAs (ncRNAs) are RNA molecules that do not code for proteins. They play various roles in gene regulation, cellular processes, and disease development. These ncRNAs can be categorized based on their length, shape, and location.

A family of microRNAs that act as direct transcriptional targets of p53, regulating key cell cycle and apoptosis processes.

A specific microRNA from the miR-34 family that represses the activity of Sirtuin 1 (SIRT1), enhancing p53 activity and promoting apoptosis.

A proto-oncogene regulated by the miR-34b seed sequence, whose 3'UTR is a binding site for miR-34b.

A long non-coding RNA that enhances p53 stability and transcriptional activity by suppressing MDM2 expression.

A long non-coding RNA that serves as a direct transcriptional target of p53, playing a key role in the repression of genes involved in cell proliferation.

A long non-coding RNA that acts as a tumor suppressor by interacting with p53 and proteins involved in cell cycle control.

A long non-coding RNA that is frequently overexpressed in various cancers due to hypomethylation. It binds to MYC, enhancing its activity and contributing to tumor progression.

A long non-coding RNA involved in regulating chromatin dynamics and promoting metastasis. It interacts with PRC2 and LSD1, repressing tumor suppressor genes and leading to EMT.

A state where the overall methylation levels in the genome are reduced. Often seen in early stages of colorectal cancer.

Specific regions in the genome where methylation changes are significantly altered in cancer. They can be classified into two groups: CIMP-low and CIMP-high.

A type of DNA methylation change associated with older age, proximal colon cancers (closer to the rectum) and a higher chance of the cancer spreading.

A process where a specific enzyme (TET) alters the existing methylation patterns, potentially leading to demethylation. It involves introducing a new chemical modification (5hmC) to the DNA.

A crucial step in the active DNA demethylation pathway. It is produced by the TET enzyme and can be further modified to ultimately remove methylation.

Mutations in these genes are more common in blood cancers. They lead to fewer 5hmC levels, potentially disrupting normal demethylation processes.

A process where the TET enzymes are not working properly in cancer, leading to incorrect methylation patterns.

This enzyme, a key player in demethylation, is often found at lower levels in colon cancer. This suggests that it plays a role in suppressing cancer development.