PGS Catalog - Berndt SI, Leukemia (2022) (Publication)

PGS Publication: PGP000448

Publication Information (EuropePMC)
Title	Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes.
PubMed ID	36273105(Europe PMC)
doi	10.1038/s41375-022-01711-0
Publication Date	Oct. 22, 2022
Journal	*Leukemia*
Author(s)	Berndt SI, Vijai J, Benavente Y, Camp NJ, Nieters A, Wang Z, Smedby KE, Kleinstern G, Hjalgrim H, Besson C, Skibola CF, Morton LM, Brooks-Wilson AR, Teras LR, Breeze C, Arias J, Adami HO, Albanes D, Anderson KC, Ansell SM, Bassig B, Becker N, Bhatti P, Birmann BM, Boffetta P, Bracci PM, Brennan P, Brown EE, Burdett L, Cannon-Albright LA, Chang ET, Chiu BCH, Chung CC, Clavel J, Cocco P, Colditz G, Conde L, Conti DV, Cox DG, Curtin K, Casabonne D, De Vivo I, Diver WR, Dogan A, Edlund CK, Foretova L, Fraumeni JF, Gabbas A, Ghesquières H, Giles GG, Glaser S, Glenn M, Glimelius B, Gu J, Habermann TM, Haiman CA, Haioun C, Hofmann JN, Holford TR, Holly EA, Hutchinson A, Izhar A, Jackson RD, Jarrett RF, Kaaks R, Kane E, Kolonel LN, Kong Y, Kraft P, Kricker A, Lake A, Lan Q, Lawrence C, Li D, Liebow M, Link BK, Magnani C, Maynadie M, McKay J, Melbye M, Miligi L, Milne RL, Molina TJ, Monnereau A, Montalvan R, North KE, Novak AJ, Onel K, Purdue MP, Rand KA, Riboli E, Riby J, Roman E, Salles G, Sborov DW, Severson RK, Shanafelt TD, Smith MT, Smith A, Song KW, Song L, Southey MC, Spinelli JJ, Staines A, Stephens D, Sutherland HJ, Tkachuk K, Thompson CA, Tilly H, Tinker LF, Travis RC, Turner J, Vachon CM, Vajdic CM, Van Den Berg A, Van Den Berg DJ, Vermeulen RCH, Vineis P, Wang SS, Weiderpass E, Weiner GJ, Weinstein S, Doo NW, Ye Y, Yeager M, Yu K, Zeleniuch-Jacquotte A, Zhang Y, Zheng T, Ziv E, Sampson J, Chatterjee N, Offit K, Cozen W, Wu X, Cerhan JR, Chanock SJ, Slager SL, Rothman N.

Released in PGS Catalog: March 24, 2023

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score ID & Name	PGS Publication ID (PGP)	Reported Trait	Mapped Trait(s) (Ontology)	Number of Variants	Ancestry distribution GWAS Dev Eval	Scoring File (FTP Link)
PGS003452 (PRS2_WM)	PGP000448 \| Berndt SI et al. Leukemia (2022)	Waldenström macroglobulinemia	Waldenstrom macroglobulinemia	2	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003452/ScoringFiles/PGS003452.txt.gz
PGS003453 (PRS43_CLL)	PGP000448 \| Berndt SI et al. Leukemia (2022)	Chronic lymphocytic leukemia	chronic lymphocytic leukemia	43	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003453/ScoringFiles/PGS003453.txt.gz
PGS003455 (PRS7_FL)	PGP000448 \| Berndt SI et al. Leukemia (2022)	Follicular lymphoma	follicular lymphoma	7	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003455/ScoringFiles/PGS003455.txt.gz
PGS003450 (PRS24_MM)	PGP000448 \| Berndt SI et al. Leukemia (2022)	Multiple myeloma	multiple myeloma	24	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003450/ScoringFiles/PGS003450.txt.gz
PGS003448 (PRS15_ALL)	PGP000448 \| Berndt SI et al. Leukemia (2022)	Acute lymphoblastic leukemia	acute lymphoblastic leukemia	15	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003448/ScoringFiles/PGS003448.txt.gz
PGS003454 (PRS5_DLBCL)	PGP000448 \| Berndt SI et al. Leukemia (2022)	Diffuse large B-cell lymphoma	diffuse large B-cell lymphoma	5	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003454/ScoringFiles/PGS003454.txt.gz
PGS003451 (PRS2_MZL)	PGP000448 \| Berndt SI et al. Leukemia (2022)	Marginal zone lymphoma	marginal zone B-cell lymphoma	2	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003451/ScoringFiles/PGS003451.txt.gz
PGS003449 (PRS21_HL)	PGP000448 \| Berndt SI et al. Leukemia (2022)	Hodgkin lymphoma	Hodgkins lymphoma	21	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003449/ScoringFiles/PGS003449.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance Metric ID (PPM)	Evaluated Score	PGS Sample Set ID (PSS)	Performance Source	Trait	PGS Effect Sizes (per SD change)	Classification Metrics	Other Metrics	Covariates Included in the Model	PGS Performance: Other Relevant Information
PPM017224	PGS003453 (PRS43_CLL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Chronic lymphocytic leukemia	OR: 2.17 [2.07, 2.28]	—	—	—	—
PPM017225	PGS003454 (PRS5_DLBCL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Chronic lymphocytic leukemia	OR: 1.33 [1.14, 1.54]	—	—	—	—
PPM017226	PGS003455 (PRS7_FL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Chronic lymphocytic leukemia	OR: 1.07 [0.98, 1.17]	—	—	—	—
PPM017227	PGS003451 (PRS2_MZL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Chronic lymphocytic leukemia	OR: 1.26 [1.09, 1.46]	—	—	—	—
PPM017228	PGS003452 (PRS2_WM)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Chronic lymphocytic leukemia	OR: 1.07 [1.01, 1.14]	—	—	—	—
PPM017229	PGS003450 (PRS24_MM)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Chronic lymphocytic leukemia	OR: 1.09 [1.02, 1.16]	—	—	—	—
PPM017230	PGS003448 (PRS15_ALL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Chronic lymphocytic leukemia	OR: 0.95 [0.9, 1.0]	—	—	—	—
PPM017231	PGS003449 (PRS21_HL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Chronic lymphocytic leukemia	OR: 1.02 [0.97, 1.08]	—	—	—	—
PPM017232	PGS003453 (PRS43_CLL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Diffuse large B-cell lymphoma	OR: 1.17 [1.12, 1.22]	—	—	—	—
PPM017233	PGS003454 (PRS5_DLBCL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Diffuse large B-cell lymphoma	OR: 2.69 [2.35, 3.08]	—	—	—	—
PPM017234	PGS003455 (PRS7_FL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Diffuse large B-cell lymphoma	OR: 1.28 [1.19, 1.39]	—	—	—	—
PPM017235	PGS003451 (PRS2_MZL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Diffuse large B-cell lymphoma	OR: 1.53 [1.34, 1.75]	—	—	—	—
PPM017236	PGS003452 (PRS2_WM)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Diffuse large B-cell lymphoma	OR: 1.24 [1.18, 1.31]	—	—	—	—
PPM017237	PGS003450 (PRS24_MM)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Diffuse large B-cell lymphoma	OR: 0.98 [0.93, 1.04]	—	—	—	—
PPM017238	PGS003448 (PRS15_ALL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Diffuse large B-cell lymphoma	OR: 0.99 [0.94, 1.04]	—	—	—	—
PPM017239	PGS003449 (PRS21_HL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Diffuse large B-cell lymphoma	OR: 1.07 [1.02, 1.13]	—	—	—	—
PPM017240	PGS003453 (PRS43_CLL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Follicular lymphoma	OR: 1.12 [1.07, 1.17]	—	—	—	—
PPM017242	PGS003455 (PRS7_FL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Follicular lymphoma	OR: 2.77 [2.52, 3.04]	—	—	—	—
PPM017243	PGS003451 (PRS2_MZL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Follicular lymphoma	OR: 1.39 [1.21, 1.61]	—	—	—	—
PPM017244	PGS003452 (PRS2_WM)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Follicular lymphoma	OR: 1.12 [1.05, 1.19]	—	—	—	—
PPM017245	PGS003450 (PRS24_MM)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Follicular lymphoma	OR: 1.01 [0.95, 1.09]	—	—	—	—
PPM017246	PGS003448 (PRS15_ALL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Follicular lymphoma	OR: 1.01 [0.95, 1.06]	—	—	—	—
PPM017247	PGS003449 (PRS21_HL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Follicular lymphoma	OR: 0.88 [0.83, 0.93]	—	—	—	—
PPM017248	PGS003453 (PRS43_CLL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Marginal zone lymphoma	OR: 1.15 [1.07, 1.24]	—	—	—	—
PPM017249	PGS003454 (PRS5_DLBCL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Marginal zone lymphoma	OR: 2.1 [1.63, 2.72]	—	—	—	—
PPM017251	PGS003451 (PRS2_MZL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Marginal zone lymphoma	OR: 2.43 [1.93, 3.06]	—	—	—	—
PPM017252	PGS003452 (PRS2_WM)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Marginal zone lymphoma	OR: 1.18 [1.07, 1.3]	—	—	—	—
PPM017253	PGS003450 (PRS24_MM)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Marginal zone lymphoma	OR: 1.05 [0.94, 1.18]	—	—	—	—
PPM017254	PGS003448 (PRS15_ALL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Marginal zone lymphoma	OR: 1.02 [0.93, 1.12]	—	—	—	—
PPM017255	PGS003449 (PRS21_HL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Marginal zone lymphoma	OR: 1.05 [0.96, 1.16]	—	—	—	—
PPM017241	PGS003454 (PRS5_DLBCL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Follicular lymphoma	OR: 1.66 [1.42, 1.94]	—	—	—	—
PPM017250	PGS003455 (PRS7_FL)	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Marginal zone lymphoma	OR: 0.94 [0.81, 1.09]	—	—	—	—

Evaluated Samples

PGS Sample Set ID (PSS)	Phenotype Definitions and Methods	Participant Follow-up Time	Sample Numbers	Age of Study Participants	Sample Ancestry	Additional Ancestry Description	Cohort(s)	Additional Sample/Cohort Information
PSS010176	—	—	20,134 individuals [ 10,629 cases , 9,505 controls ]	—	European	—	NR	Inter- Lymph Consortium