chr13·hg38·114.4 Mb

Chromosome 13

The genome's quiet desert — gene-poor, repeat-rich, and home to two of the most iconic tumor suppressors in cancer biology.

Physical Properties

Length114.4 Mb

Centromereacrocentric

p-arm16.0 Mb

q-arm96.3 Mb

GC content38.5%

Genomic Features

Protein-coding genes327

Gene density2.9 / Mb

CpG islands7,573

EPIC v2 probes28,249

Notable

Largest genePCDH9 (940 kb)

Disease associations

Retinoblastoma

Breast/ovarian cancer (BRCA2)

Wilson disease

· RB1 was the first tumor suppressor gene identified (1986)

· Acrocentric — involved in Robertsonian translocations

· Contains BRCA2, key to homologous recombination repair

Genomic Architecture

LINEs — Heavily enriched relative to genome average, consistent with GC-poor composition. LINE-1 (L1) elements are particularly abundant in the gene desert regions

SINEs/Alu — Relatively depleted compared to gene-rich chromosomes, following the well-established inverse correlation between Alu density and LINE density

Total repetitive content — Approximately 50% of chromosome 13 sequence is repetitive

Deep Cuts

The oncomiR duality — Chromosome 13 is the only human chromosome that harbors both a classic tumor-suppressor miRNA cluster (miR-15a/16-1, deleted in CLL) and the first identified oncogenic miRNA cluster (miR-17-92, amplified in lymphomas)…

The gene desert paradox — Despite having one of the lowest gene densities of any autosome, trisomy 13 (Patau syndrome) is more lethal than trisomy 18 (which has more genes). The severity likely stems from specific developmental master regulato…

The Robertsonian highway — The rob(13;14) translocation is the single most common balanced chromosomal rearrangement in humans (1:1,300), yet it was only in 2022 that the actual breakpoint sequences in the short arms were resolved by the T2T Co…

§ Deep dive

LINEsHeavily enriched relative to genome average, consistent with GC-poor composition. LINE-1 (L1) elements are particularly abundant in the gene desert regions

SINEs/AluRelatively depleted compared to gene-rich chromosomes, following the well-established inverse correlation between Alu density and LINE density

Total repetitive contentApproximately 50% of chromosome 13 sequence is repetitive

FRA13A(13q13.2): Maps within the neurobeachin (NBEA) gene, spanning ~730 kb. Notably situated between two major tumor suppressors — BRCA2 at 13q13.1 and RB1 at 13q14.2 — making this region a hotspot for deletions in solid tumors

FRA13BAdditional fragile site contributing to chromosomal instability in cancer genomes