Discovery of novel predisposing coding and noncoding variants in familial Hodgkin lymphoma

Abstract

Familial aggregation of Hodgkin lymphoma (HL) has been demonstrated in large population studies, pointing to genetic predisposition to this hematological malignancy. To understand the genetic variants associated with the development of HL, we performed whole genome sequencing on 234 individuals with and without HL from 36 pedigrees that had 2 or more first-degree relatives with HL. Our pedigree selection criteria also required at least 1 affected individual aged <21 years, with the median age at diagnosis of 21.98 years (3-55 years). Family-based segregation analysis was performed for the identification of coding and noncoding variants using linkage and filtering approaches. Using our tiered variant prioritization algorithm, we identified 44 HL-risk variants in 28 pedigrees, of which 33 are coding and 11 are noncoding. The top 4 recurrent risk variants are a coding variant in KDR (rs56302315), a 5' untranslated region variant in KLHDC8B (rs387906223), a noncoding variant in an intron of PAX5 (rs147081110), and another noncoding variant in an intron of GATA3 (rs3824666). A newly identified splice variant in KDR (c.3849-2A>C) was observed for 1 pedigree, and high-confidence stop-gain variants affecting IRF7 (p.W238∗) and EEF2KMT (p.K116∗) were also observed. Multiple truncating variants in POLR1E were found in 3 independent pedigrees as well. Whereas KDR and KLHDC8B have previously been reported, PAX5, GATA3, IRF7, EEF2KMT, and POLR1E represent novel observations. Although there may be environmental factors influencing lymphomagenesis, we observed segregation of candidate germline variants likely to predispose HL in most of the pedigrees studied.

Graphical abstract

Figure 1.

Families with putative germ line variants. (A) Study overview and prioritization schema. (B) Counts of coding variants according to prioritization category overall and per pedigree. (C) Heat map of coding variants showing the number of carriers across pedigrees, the ClinVar rating, the variant classification based on American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines, and taking into account evidence of familial segregation and a possible predisposition to HL and the priority level based on our prioritization schema as described in Panel A. (D) Counts of noncoding variants according to prioritization category overall and per pedigree. (E) Heat map of noncoding variants showing recurrence across pedigrees. ncRNA, noncoding RNA; ∗pedigrees with early-onset; † the variant is within 1 logarithm of the odds (1-LOD) multipoint logarithm of the odds (MLOD) region.

Figure 2.

Pedigrees of families with a high frequency of HL. Pedigree representation of the 36 families included for analysis. Variants listed segregate with the disease phenotype and obligate carriers within each pedigree. HL16594: TCF3-p.E496K and HBS1L-p.I388V demonstrate potential codominant inheritance; HL213: RAD51D-p.G192D; HL533: ARMC9-p.K423Rfs∗29; HL696: TRPG1-p.Y61∗; HL2350: KDR-p.A1065T; HL2408: POLR1E-p. R149∗ and CDT1-c.1477+3_1477+24del† (limited support of alternative allele for father of proband); HL2491: KLHDC8B-c.-1108C>T and GATA3-intronic; HL2576: no variant; HL2696: EFR3B-p.Q285∗; HL2694: EEF2KMT-p.K177∗; HL3056: no variant; HL3262: KDR-p.A1065T, DDX10-p.K687∗, EIF1AD-c.88-4C>G; HL4479: BAD-p.K133Q, CLEC16A-p.R860C; HL3402: IRF7-p.W238∗; HL4450: KLHDC8B-c.1108C>T; HL4643: IRF8-intronic; HL3929: POT1-p.D224N and GATA3-intronic; HL4897: no variant; HL4968: no variant; HL5140: no variant; HL5171: MAP3K7-p.V428I and MET-p.P791L; HL5215: no variant; HL6898: PAX5-intronic(3)∗; HL1000001: MST1R-p.V233Cfs∗16; HL1000003: PAX5-intronic(3)∗; HL1000007: BLK-c.369-2A>G and GPNMB-c.367+2T>C; HL1000008: no variant; HL1000056: REL-p.H307R; HL1000059: GSN-p.W554∗ and IGSF10-p.S1099∗; HL1000060: ACOT8-c.488+1G>A, CARD9-c.184+1G>A, MROH2A-c.4452+1G>A, and ZNF683-p.R35∗; HL1000061: no variant; HL1000063: KLHDC8B-c.1108C>T; HL1000064: KDR-c.3849-2A>C and RUNX3-intergenic; HL1000065: ATF3-intronic and MYB-intergenic; and HL1000078: JUNB-p.P112S and POLR1E-p.L283Sfs∗9. WT, wild-type.

Figure 2.

Pedigrees of families with a high frequency of HL. Pedigree representation of the 36 families included for analysis. Variants listed segregate with the disease phenotype and obligate carriers within each pedigree. HL16594: TCF3-p.E496K and HBS1L-p.I388V demonstrate potential codominant inheritance; HL213: RAD51D-p.G192D; HL533: ARMC9-p.K423Rfs∗29; HL696: TRPG1-p.Y61∗; HL2350: KDR-p.A1065T; HL2408: POLR1E-p. R149∗ and CDT1-c.1477+3_1477+24del† (limited support of alternative allele for father of proband); HL2491: KLHDC8B-c.-1108C>T and GATA3-intronic; HL2576: no variant; HL2696: EFR3B-p.Q285∗; HL2694: EEF2KMT-p.K177∗; HL3056: no variant; HL3262: KDR-p.A1065T, DDX10-p.K687∗, EIF1AD-c.88-4C>G; HL4479: BAD-p.K133Q, CLEC16A-p.R860C; HL3402: IRF7-p.W238∗; HL4450: KLHDC8B-c.1108C>T; HL4643: IRF8-intronic; HL3929: POT1-p.D224N and GATA3-intronic; HL4897: no variant; HL4968: no variant; HL5140: no variant; HL5171: MAP3K7-p.V428I and MET-p.P791L; HL5215: no variant; HL6898: PAX5-intronic(3)∗; HL1000001: MST1R-p.V233Cfs∗16; HL1000003: PAX5-intronic(3)∗; HL1000007: BLK-c.369-2A>G and GPNMB-c.367+2T>C; HL1000008: no variant; HL1000056: REL-p.H307R; HL1000059: GSN-p.W554∗ and IGSF10-p.S1099∗; HL1000060: ACOT8-c.488+1G>A, CARD9-c.184+1G>A, MROH2A-c.4452+1G>A, and ZNF683-p.R35∗; HL1000061: no variant; HL1000063: KLHDC8B-c.1108C>T; HL1000064: KDR-c.3849-2A>C and RUNX3-intergenic; HL1000065: ATF3-intronic and MYB-intergenic; and HL1000078: JUNB-p.P112S and POLR1E-p.L283Sfs∗9. WT, wild-type.

Figure 2.

Pedigrees of families with a high frequency of HL. Pedigree representation of the 36 families included for analysis. Variants listed segregate with the disease phenotype and obligate carriers within each pedigree. HL16594: TCF3-p.E496K and HBS1L-p.I388V demonstrate potential codominant inheritance; HL213: RAD51D-p.G192D; HL533: ARMC9-p.K423Rfs∗29; HL696: TRPG1-p.Y61∗; HL2350: KDR-p.A1065T; HL2408: POLR1E-p. R149∗ and CDT1-c.1477+3_1477+24del† (limited support of alternative allele for father of proband); HL2491: KLHDC8B-c.-1108C>T and GATA3-intronic; HL2576: no variant; HL2696: EFR3B-p.Q285∗; HL2694: EEF2KMT-p.K177∗; HL3056: no variant; HL3262: KDR-p.A1065T, DDX10-p.K687∗, EIF1AD-c.88-4C>G; HL4479: BAD-p.K133Q, CLEC16A-p.R860C; HL3402: IRF7-p.W238∗; HL4450: KLHDC8B-c.1108C>T; HL4643: IRF8-intronic; HL3929: POT1-p.D224N and GATA3-intronic; HL4897: no variant; HL4968: no variant; HL5140: no variant; HL5171: MAP3K7-p.V428I and MET-p.P791L; HL5215: no variant; HL6898: PAX5-intronic(3)∗; HL1000001: MST1R-p.V233Cfs∗16; HL1000003: PAX5-intronic(3)∗; HL1000007: BLK-c.369-2A>G and GPNMB-c.367+2T>C; HL1000008: no variant; HL1000056: REL-p.H307R; HL1000059: GSN-p.W554∗ and IGSF10-p.S1099∗; HL1000060: ACOT8-c.488+1G>A, CARD9-c.184+1G>A, MROH2A-c.4452+1G>A, and ZNF683-p.R35∗; HL1000061: no variant; HL1000063: KLHDC8B-c.1108C>T; HL1000064: KDR-c.3849-2A>C and RUNX3-intergenic; HL1000065: ATF3-intronic and MYB-intergenic; and HL1000078: JUNB-p.P112S and POLR1E-p.L283Sfs∗9. WT, wild-type.

Figure 3.

Recurrent noncoding variants. (A) The PAX5 intronic variant (rs147081110) overlaps an ENCODE DNase I hypersensitivity peak cluster along with an ENCODE 3 transcription factor chromatin immunoprecipitation sequencing cluster and has FIMO-predicted loss of XBP1 binding. (B) The GATA3 intronic variant (rs3824666) overlaps an ENCODE DNase I hypersensitivity peak cluster along with an ENCODE 3 transcription factor chromatin immunoprecipitation sequencing cluster and has FIMO-predicted loss of binding of TCF3 and TCF12.

Figure 4.

LOF variants falling under maximum multipoint linkage regions in large HL pedigrees. (A) Segregation of IRF7-p.W238∗ among 4 affected relatives in HL3402. (B) MLOD plot on chromosome 11 with IRF7 location indicated. (C) Protein paint diagram showing the location of stop-gain variant p.W238∗, which could result in the removal of the IRF-3 functional domain. (D) Segregation of EEF2KMT-p.K177∗ among 2 affected relatives and 2 obligate carriers in HL3402. Two unaffected siblings also carry the variant. (E) MLOD plot on chromosome 16 with the EEF2KMT location indicated. (F) Protein paint diagram showing the location of stop-gain variant p.K177∗, which could result in the removal of part of the AdoMet_MTases functional domain.