Objective: The objective of this study is two-fold: 1) to evaluate and compare bone marrow and peripheral blood samples collected from individuals diagnosed with an inherited bone marrow failure syndrome for copy number variations; 2) to compare genome-wide SNP arrays and cytogenetics: two methods of detecting chromosomal variations.
Methods: 185 DNA samples from 85 individuals were genotyped by genome-wide SNP array (~1M SNPs). Each of the 85 individuals had at least one bone marrow sample drawn and genotyped and nine individuals had serial bone marrow collections. There were 69 matched bone marrow-peripheral blood pairs from 53 individuals. Karyotyping was performed on each of the 114 total bone marrow samples, and FISH was carried out on 26 bone marrow samples from 18 individuals. The 85 individuals were diagnosed with Fanconi anemia (18), telomere biology disorder (38), Diamond-Blackfan anemia (15), Shwachman-Diamond syndrome (7), Thrombocytopenia-absent radius (TAR) syndrome (1), GATA2 deficiency syndrome (3), or unaffected relatives (3).
Results: Genome-wide SNP array analysis of the 69 matched bone marrow and peripheral blood from 53 individuals showed that 48 individuals (58 pairs) did not exhibit any discernible differences in copy number variations nor any indication of mosaic chromosomal events. Five individuals (11 sample pairs) exhibited at least one mosaic event, and in four (nine sample pairs) there was a discernible difference in the mosaicism frequency between the bone marrow and peripheral blood samples. In each instance, the bone marrow exhibited a higher frequency of mosaicism than the peripheral blood. One individual (two sample pairs), diagnosed with Fanconi anemia, exhibited copy number-neutral isodisomy at the chromosome 16 terminus, including FANCA, and each sample exhibited the same degree of isodisomy.
Of the 114 bone marrow samples that were analyzed by karyotyping, 68 exhibited an anomaly in at least one cell. SNP array results matched the cytogenetics results from 37/68 samples, while 31/68 samples displayed an anomaly by cytogenetics that was not observed by SNP array. Of the 31 samples with discordant results, 18 abnormal karyotypes were detected in either one or two cells, and only two were detected in more than six cells. The two discordant anomalies detected at a high frequency, 14/20 cells and 20/20 cells, were characterized as an inversion and translocation, both balanced rearrangements undetectable by SNP array.
Conclusion: Unbalanced, chromosomal mosaic events were detected in both bone marrow and peripheral blood in as low as 10% of cells, but serial samples confirm that anomalies are detected earlier in bone marrow. Genome-wide SNP arrays are sensitive to low-level somatic mosaicism, similarly to cytogenetics, but can identify more chromosomal changes of varying sizes. The primary discrepancy is the inability to detect balanced chromosome anomalies.
Clinical applicability: Knowing the specific sensitivities and potential limitations of evaluating bone marrow and peripheral blood, as well as the strengths and weaknesses of utilizing genome-wide SNP array vs cytogenetics, can enable earlier detection and better-informed hematologic disease management.
No relevant conflicts of interest to declare.
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