SNP-Array Karyotyping Reveals the Presence of Previously Cryptic Clonal Chromosomal Aberrations Including Segmental UPD in Patients with Fanconi Anemia.
Authors: Wlodarski Marcin , Toennies Holger , Dunbar Andrew , Nearman Zach , Nagy Marion , Kuehl Joern-Sven , Neitzel Heidemarie , Ebell Wolfram , Maciejewski Jaroslaw 
Published: April 2020

Fanconi anaemia (FA) is a multigenic chromosomal (chr) instability syndrome characterized by a wide array of congenital defects and early predisposition to bone marrow (BM) failure and solid tumors. Most frequent hematologic complications are aplastic anemia (AA) or myelodysplasia (MDS) with a high AML transformation rate. Genomic instability resulting from impaired DNA crosslink repair in FA may lead to unbalanced chr aberrations that can be detected in clonally expanding BM stem cells. Most frequent abnormalities include gain1q, del 7 and gain3q, the latter two are associated with a poor prognosis. Due to low resolution of metaphase cytogenetics (MC) and its dependence upon in-vitro cell growth, detection of chr lesions is often limited or non-informative. High-density SNP arrays (SNPA) can be used for a very precise identification of unbalanced genomic lesions and copy-neutral LOH. We hypothesize that using SNPA previously cryptic clonal genomic aberrations can be detected in some FA patients and their characterization may help predict propensity to transformation and point towards pathogenetic lesions. We applied Affymetrix 250K SNP-A to investigate patients with FA (N=21: 15 FANCA, 4 FANCG and 2 FANCC; avg age: 12y) and as controls healthy BM transplant donors (n=50). For comparison, non-FA patients with AA (n=68), MDS (n=98) and secondary AML (n=30) were analyzed. Lesions spanning more than 100 SNPs were defined as significant. Copy number polymorphisms detected in controls and public data bases were not considered pathologic. Globally, MC was abnormal in 48% of FA patients while SNP-karyotyping revealed chr lesions in 85% of patients. The additional lesions detected by SNPA included monosomy 7, deletions (1,5,6,11,12,22,18,20) and gains (1,3,4,21). For most FA patients comparative genomic hybridization and FISH were performed and confirmed genomic gains and losses detected by SNPA. In addition, using SNPA, copy number-neutral LOH, segmental uniparental disomy (UPD) was identified in 43% of FA patients on various chr (2,3,4,6,8,9,11,13,16,18). By comparison tin AA, MDS and AML, UPD was present in 31%, 21% and 23%, respectively. Next, patients with known recurrent defects were analyzed with regard to the presence of additional UPD, which was detected in 50% of patients with gain on chr.3q vs. in 38% of patients without gain3q, 50% of patients with vs. 36% without gain1q, and in 42% of patients with vs. 28% without del 7, respectively. On 3 FA patients with advanced MDS (RAEBt; n=2) and AA (n=1) SNPA was performed on archived samples collected prior to progression into AML. In all these patients clonal chr aberrations were detected, including various previously cryptic lesions (gain4q, gain21q, UPD on 8q and 9p). Our study represents the first application of high-density SNPA for karyotyping of patients with FA and demonstrates that this method may uncover cryptic clonal chr lesions, including copy number neutral LOH due to UPD. This type of lesion is a novel finding in FA. Further studies are required to determine the functional significance of these lesions and their correlation with leukemia or solid tumors.