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Page 190 Feusier et al. J Transl Genet Genom 2021;5:189-99 https://dx.doi.org/10.20517/jtgg.2021.05

Conclusion: SGS analysis of an extended high-risk CLL pedigree identified the most significant evidence to-date for
a 0.9 Mb CLL disease locus at 2q22.1, harboring CXCR4. This discovery contributes to a growing literature
implicating CXCR4 in inherited risk to CLL. Investigation of the segregating haplotype in the pedigree will be
valuable for elucidating risk variant(s).

Keywords: Gene-mapping, chronic lymphocytic leukemia (CLL), linkage, CXCR4, shared genomic segment (SGS),
pedigree, Utah Population Database (UPDB)

INTRODUCTION
Chronic lymphocytic leukemia (CLL) is the most common adult leukemia diagnosed in individuals of
[1]
European ancestry in the United States (5.0/100,000) . CLL has a strong heritable component, and first-
degree relatives have a 7.5-8.5 fold elevated risk of developing CLL . Therefore, a family-based design is
[2-4]
relevant to consider for CLL. However, because CLL is relatively rare, this design presents a challenge in
ascertainment of multi-case families. Translational relevance for successful family discoveries includes
genetic counselling for at-risk family members and new avenues for understanding biological mechanism
towards improved prevention and treatment.

An established family-based statistical approach is linkage analysis. Recombination events are estimated in
families which localize regions, and risk haplotypes, which are inherited to affect family members. These
haplotypes can subsequently be interrogated to identify specific variants involved in disease pathogenesis.
This design boosts power for rarer risk alleles which are enriched in the family setting. In the study of
familial CLL, five genome-wide linkage studies have been performed thus far . Of these, only one locus
[5-9]
has been proposed with genome-wide significance. Linkage analyses in 206 CLL families identified a
significant peak at chromosome 2q21.2 (LOD-equivalent 3.11, P = 7.7 × 10 ), and a 1-LOD support interval
-5
[7]
defining a ~6.25 Mb locus at 2q21.2-2q22.1 . The locus contains the gene CXCR4 (C-X-C chemokine
receptor type 4) (at 2q22.1), of particular interest due to its key role in B cell lymphopoiesis and
maintenance of immature B cells in the bone marrow.

Two family-based whole exome sequencing (WES) studies have been performed [10,11] . Rigorous statistical
thresholds that account for the multiple phases and family-based expectations have not yet been defined for
direct-to-sequencing family studies, hence these studies remain largely observational in nature. The prior
studies focused on finding recurrent rare alleles in families, but the segregation of those alleles was not
formally assessed (i.e., how probabilities for the findings are influenced by allele frequency, non-sharing in
cases, and unaffected carriers). In a study of 59 small families, Goldin et al. , focused on identifying coding
[10]
variants recurrent within and shared across at least two families. They identified 6 families recurrent for an
allele in ITGB2 [rs2230531 at 21q22.3, minor allele frequency (MAF) = 0.007]. However, recurrence of this
[12]
variant was not replicated in a follow-up study of ITGB2 in 47 small families . In a WES study of 66
families (no restriction made to sharing across multiple families), ITGB2 variants were not identified, but
four different coding variants were found to be recurrent within 7 different small families, all in genes
involving the shelterin complex (four in POT1, one in ACD and two TERF2IP at 7q31.33, 16q22.1 and
16q23.1, respectively) .
[11]

One family study used genome-wide genotype data to identify germline copy number variants (CNV) in
CLL families occurring at regions known to be commonly aberrant in malignant CLL cells. This identified
two germline CNVs: a mutation at 13q involving DLEU7 and a gain at 6p including IRF4. Each was shared
by a single CLL sib-pair . These findings have yet to be replicated.
[13]