Secondary malignant neoplasm

Summary

Secondary malignant neoplasm (MONDO:0024881) is a cancer with 23 GWAS associations across 84 studies and 4 clinical trials. Top therapeutic interventions include lufenuron. A subtype of cancer — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Classification: Cancer
• GWAS associations: 23
• Clinical trials: 4

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	secondary malignant neoplasm
Mondo ID	MONDO:0024881
EFO	EFO:0009812
NCIT	C4968
SNOMED CT	128462008
UMLS	C3266877
MedGen	473807
Is cancer (heuristic)	yes

Also known as: secondary cancer · secondary malignancy · secondary malignant neoplasm

Data availability: 23 GWAS associations (84 studies).

Disease family

This is a subtype of cancer. Genetic, therapeutic, and trial evidence is largely curated at the broader-term level — see the parent page for the associated-gene cohort and molecular evidence.

Classification path: disease › human disease › disease by etiologic mechanism › cancer or benign tumor › neoplastic disease or syndrome › neoplasm › cancer › secondary malignant neoplasm

Related subtypes (32): respiratory system cancer, immune system cancer, musculoskeletal system cancer, integumentary system cancer, peritoneum cancer, cardiovascular cancer, reproductive system cancer, malignant giant cell tumor, digestive system cancer, lipomatous cancer, thoracic cancer, malignant glomus tumor, malignant mesenchymoma, carcinoma, sarcoma, blastoma, head and neck cancer, malignant mixed neoplasm, nervous system cancer, retroperitoneal cancer, malignant germ cell tumor, malignant mesothelioma, malignant urinary system neoplasm, childhood malignant neoplasm, anaplastic cancer, malignant spindle cell neoplasm, high grade malignant neoplasm, malignant endocrine neoplasm, malignant soft tissue neoplasm, refractory malignant neoplasm, malignant adenoma, cancer of unknown primary site

Subtypes (2): secondary carcinoma, metastatic malignant neoplasm

Genetics & variants

GWAS landscape

23 GWAS associations across 84 studies. Top hits map to 19 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs143290448	9e-14	KIF2B - ISCA1P3	G	3.18
rs149229477	2e-13	FNIP2	C	2.42
rs545673517	4e-13	METTL15	T	3.13
rs138790055	2e-12	ADGRL2 - LINC01362	C	1.97
rs190319432	3e-12	LINC03142	G	2.54
rs547614934	3e-12	HBG2, OR51B5, HBE1	C	2.71
rs575123534	3e-12	CRAT37	A	2.22
rs554856398	6e-12	KNSTRN - IVD	T	2.55
rs576199011	1e-11	LINC01508	C	3.41
rs565728517	2e-11	Y_RNA - LINC01896	G	3.6
rs146223400	3e-11	COL4A3	G	2.31
rs533972607	3e-11	TENM3	A	3.38
rs569410606	3e-11	SLC25A16	G	2.31
rs552524684	3e-11	NRG1	C	2.81
rs190717272	4e-11	ATP6AP1L - RPL5P16	A	2.95
rs185547104	4e-11	HMCN1 - PRG4	C	2.07
rs540545084	2e-10	SGCZ	?
rs139215866	1e-07	LINP1	?
rs559388549	3e-07	LINC01725, LINC01362	?
rs75892473	3e-07	RNA5SP144 - LARP7P4	?
rs145343626	4e-07	MRPS30 - HCN1	?
rs190635857	4e-07	LINC01517, LINC00837	?
rs146749209	2e-06	PARP11	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90477229	Verma A	2024	16,934	428,114	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90435630	Zhou W	2018	9,483	370,604	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90079620	Backman JD	2021	7,019	380,863	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90083606	Backman JD	2021	7,019	380,863	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90079625	Backman JD	2021	6,526	381,309	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90083611	Backman JD	2021	6,526	381,309	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90435631	Zhou W	2018	5,379	370,604	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90079629	Backman JD	2021	5,376	382,352	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90083615	Backman JD	2021	5,376	382,352	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90477228	Verma A	2024	4,003	116,401	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

Tier	Variants
Tier 1: coding	0
Tier 2: splice/UTR	0
Tier 3: regulatory	0
Tier 4: intronic/intergenic	23

MAF distribution

Bucket	Variants
common (>=0.05)	2
low_freq (0.01-0.05)	0
rare (<0.01)	16
unknown	5

Functional consequences

Consequence	Count
intron_variant	18
intergenic_variant	4
non_coding_transcript_exon_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs143290448	17	53865695	G>A,C,T	0.001	intron_variant	KIF2B - ISCA1P3	9e-14	Tier 4: intronic/intergenic
rs149229477	4	158891187	C>G,T	0.001	intron_variant	FNIP2	2e-13	Tier 4: intronic/intergenic
rs545673517	11	28292358	T>C	0	intron_variant	METTL15	4e-13	Tier 4: intronic/intergenic
rs138790055	1	82417254	C>T	0.002	intron_variant	ADGRL2 - LINC01362	2e-12	Tier 4: intronic/intergenic
rs190319432	9	22944285	G>A,C	0.001	intron_variant	LINC03142	3e-12	Tier 4: intronic/intergenic
rs547614934	11	5485952	C>T	0	intron_variant	HBG2, OR51B5, HBE1	3e-12	Tier 4: intronic/intergenic
rs575123534	15	91431325	A>G,T	0.001	intron_variant	CRAT37	3e-12	Tier 4: intronic/intergenic
rs554856398	15	40401957	T>C	0	intergenic_variant	KNSTRN - IVD	6e-12	Tier 4: intronic/intergenic
rs576199011	9	90390722	C>A,T	0.001	intron_variant	LINC01508	1e-11	Tier 4: intronic/intergenic
rs565728517	18	78687251	G>A	0	intron_variant	Y_RNA - LINC01896	2e-11	Tier 4: intronic/intergenic
rs146223400	2	227175597	G>A	0.001	intron_variant	COL4A3	3e-11	Tier 4: intronic/intergenic
rs533972607	4	182541965	A>C	0	intron_variant	TENM3	3e-11	Tier 4: intronic/intergenic
rs569410606	10	68507323	G>A,C,T	0.001	intron_variant	SLC25A16	3e-11	Tier 4: intronic/intergenic
rs552524684	8	31971492	C>T	0	intron_variant	NRG1	3e-11	Tier 4: intronic/intergenic
rs190717272	5	82518073	A>G	0.001	intron_variant	ATP6AP1L - RPL5P16	4e-11	Tier 4: intronic/intergenic
rs185547104	1	186267113	C>G	0.001	intergenic_variant	HMCN1 - PRG4	4e-11	Tier 4: intronic/intergenic
rs540545084	8	14685503	C>A		intron_variant	SGCZ	2e-10	Tier 4: intronic/intergenic
rs139215866	10	6761712	G>C,T		intron_variant	LINP1	1e-07	Tier 4: intronic/intergenic
rs559388549	1	83075722	CCTT>C		intron_variant	LINC01725, LINC01362	3e-07	Tier 4: intronic/intergenic
rs75892473	3	144717893	A>T	0.05	intergenic_variant	RNA5SP144 - LARP7P4	3e-07	Tier 4: intronic/intergenic
rs145343626	5	44923826	C>T		intergenic_variant	MRPS30 - HCN1	4e-07	Tier 4: intronic/intergenic
rs190635857	10	28792906	A>T	0.05	non_coding_transcript_exon_variant	LINC01517, LINC00837	4e-07	Tier 4: intronic/intergenic
rs146749209	12	3865319	C>T		intron_variant	PARP11	2e-06	Tier 4: intronic/intergenic

Genes & proteins

No associated-gene cohort resolved for this disease. Atlas builds the molecular and therapeutic sections — associated genes, protein families, druggability, pathways, interactions, and drug associations — by aggregating over a disease’s associated genes (resolved via GWAS / GenCC / ClinVar / CIViC), and none resolved here. This is expected for antibody-mediated, autoimmune, or otherwise non-gene-defined conditions; the curated evidence for this disease is its clinical features, GWAS susceptibility, and clinical trials (above).

Function

No pathway enrichment — requires an associated-gene cohort.

Therapeutics

No druggable-target or therapeutic data for this disease’s cohort.

Clinical trials & evidence

Clinical trials

Clinical trials: 4.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	3
PHASE2	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT02530515	PHASE2	COMPLETED	Ex Vivo-activated Autologous Lymph Node Lymphocytes in Treating Patients With Chronic Lymphocytic Leukemia
NCT05578274	Not specified	NOT_YET_RECRUITING	Abscopal Effect from Low-dose Radiotherapy in Metastatic Cancer Combined with Stereotactic Body Radiotherapy
NCT05733156	Not specified	RECRUITING	Abscopal Effect from the Low-dose Radiotherapy in Polymetastatic Cancer Patients Receiving Stereotactic Radiotherapy
NCT05832138	Not specified	NOT_YET_RECRUITING	ONLOOP Trial: Evaluating a New Surveillance and Support System for Survivors of Childhood Cancer in Ontario

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
LUFENURON	2	1