PMC6702516_01
Molecular diagnosis of Shwachman-Diamond syndrome in a pediatric patient. Targeted sequencing of pre-leukemia blood DNA and (A) whole exome sequencing analysis of buccal swab DNA at AML diagnosis reveal compound heterozygous mutations impacting SBDS gene, consistent with an autosomal recessive Shwachman-Diamond syndrome. (B) Schematic representation of SBDS coding sequence (NM_016038), with confirmed c.120delG (exonic), and c.258+2T>C (intronic/splicing) mutations.
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F1
A point mutation in IDH1 (c.394C>T/p.Arg132Cys), reported to be pathogenic and recurrent in adult AML and other cancer types, was identified both by exome and transcriptome sequencing, with both wild-type and mutant alleles expressed at 45 and 55%, respectively (Figure 3A, Figure S1 and data not shown). IDH mutation appearance, we performed NGS on DNA material obtained from scraping fixed bone-marrow smears, archived 6 months prior to AML diagnosis. IDH1 c.394C>T (p.Arg132Cys) mutation was not detected in any of the 44 sequencing reads obtained spanning that position, indicating that the mutation was not present or below our detection threshold 6 months prior to AML diagnosis (Figure S1).
Molecular profiling of SDS-associated leukemia. (A) Differential whole exome sequencing analyses of leukemic bone marrow cell DNA compared with normal control (e.g., buccal swab DNA) reveal a somatic mutation (c.394C>T) in IDH1 coding sequence, corresponding to the recurrent p.Arg132Cys mutation reported in adult AML. (B) Schematic representation of IDH1 coding sequence (NM_005896) and Sanger sequencing chromatogram confirming the c.394C>T (p.Arg132Cys) mutation in leukemic bone marrow cell DNA.
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F3
A point mutation in IDH1 (c.394C>T/p.Arg132Cys), reported to be pathogenic and recurrent in adult AML and other cancer types, was identified both by exome and transcriptome sequencing, with both wild-type and mutant alleles expressed at 45 and 55%, respectively (Figure 3A, Figure S1 and data not shown). The mutation was confirmed by Sanger sequencing (Figure 3B). S1). Somatic mutation of IDH1 defined a major leukemic clone (variant allele fraction of 0.38 for a specimen with ~80% leukemic infiltration) while a minor clone with a mutation in BRCA2 (variant allele fraction of 0.08) was also detected (Figure 3A).