Figure 3.
Schematic representation of the novel GATA2 enhancer variant and expression allelic imbalance. (A) Diagram of the GATA2 locus with the relative positions of the GATA2 gene (orange), the minimal translocated super enhancer region,16,17,19,29,30 corresponding to the −110 region enhancer containing the unique A-to-T variant (GRCh38.p7 chr3:128,604,048) and neighboring LINC01565 and RPN genes. (B) Genomic sequence with the RefSeq and novel family variant is indicated (red font). The position of the E-box (yellow highlight), GATA-box (green highlight), and composite element (red underline) are indicated. (C) Diagram of the haplomap for the patients and their parents based on WGS and direct DNA sequencing (refer to supplemental Tables 1-2). The chromosome strands are indicated by color with the shared enhancer strand among carrier and affected individuals colored red. The position and genotype of the unique enhancer variant are indicated with the nucleotide base and red arrowhead. Each other color represents the other GATA2 allele within each respective individual. The relative position and genotype of the fiducial SNP rs2335052 is also indicated. The rs2335052 population has a variant allele frequency of ∼20% (dbSNP Build 155), and it has no known clinical significance (ClinVar ID# 134467). (D) Direct DNA sequencing traces from gDNA (control) and cDNA from stem cells (CD34+), monocytes (CD14+), granulocytes, and PBL. The relative signal intensity for the guanine (G) (black) and adenine (A) (green) bases at rs2335052 (arrows) are given below each sample trace as a percent of total signal for all 4 nucleotide bases. The International Union of Pure and Applied Chemistry notation is used to designate nucleotide sequence.

Schematic representation of the novel GATA2 enhancer variant and expression allelic imbalance. (A) Diagram of the GATA2 locus with the relative positions of the GATA2 gene (orange), the minimal translocated super enhancer region,16,17,19,29,30 corresponding to the −110 region enhancer containing the unique A-to-T variant (GRCh38.p7 chr3:128,604,048) and neighboring LINC01565 and RPN genes. (B) Genomic sequence with the RefSeq and novel family variant is indicated (red font). The position of the E-box (yellow highlight), GATA-box (green highlight), and composite element (red underline) are indicated. (C) Diagram of the haplomap for the patients and their parents based on WGS and direct DNA sequencing (refer to supplemental Tables 1-2). The chromosome strands are indicated by color with the shared enhancer strand among carrier and affected individuals colored red. The position and genotype of the unique enhancer variant are indicated with the nucleotide base and red arrowhead. Each other color represents the other GATA2 allele within each respective individual. The relative position and genotype of the fiducial SNP rs2335052 is also indicated. The rs2335052 population has a variant allele frequency of ∼20% (dbSNP Build 155), and it has no known clinical significance (ClinVar ID# 134467). (D) Direct DNA sequencing traces from gDNA (control) and cDNA from stem cells (CD34+), monocytes (CD14+), granulocytes, and PBL. The relative signal intensity for the guanine (G) (black) and adenine (A) (green) bases at rs2335052 (arrows) are given below each sample trace as a percent of total signal for all 4 nucleotide bases. The International Union of Pure and Applied Chemistry notation is used to designate nucleotide sequence.

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