A polymorphism of the X-linked gene IDS increases the number of females informative for transcriptional clonality assays

Abstract

Studies of clonality have been essential for understanding the hierarchy of hematopoi-esis and the biology of malignancies. Most clonality assays are based on the X chromosome inactivation phenomenon in females; these assays detect protein polymorphisms, differences in DNA methylation, or transcripts of the active X chromosome. Assays based on protein polymorphisms or DNA methylation have significant shortcomings. The major disadvantage of transcriptional assays is their limited applicability since only approximately half of females are informative for these studies. We have developed a new tran-scriptional assay based on an exonic polymorphism of the X-chromosome gene IDS. This gene is located in the same X-chromosome region (Xq28) as G6PD and p55, two genes with exonic polymorphisms for which we previously developed transcriptional assays. We developed non-radioactive PCR-based assays for rapid screening of genotype and determination of clonality. We also report reaction conditions for a quantitative ligase detection assay of IDS allelic transcripts. The frequency of the IDS polymorphism is 46% in Caucasian females and 39% in African-American females; in combination with G6PD and p55, 76% of Caucasian females and 62% of African-American females are informative for these assays. While this gene is highly polymorphic in Caucasian and African-American females, it is not informative in Oriental females. We established that the IDS gene is in linkage equilibrium with G6PD and p55. Unlike methylation-based assays, this assay is suitable for studying clonality in non-nucleated cells such as platelets and reticulocytes. With the discovery of exonic polymorphisms of other X-chromosome genes, all females should eventually be suitable for X-chromosome transcriptional clonality analysis. Am.

Aberrant Expression of X-Linked Genes RbAp46, Rsk4, and Cldn2 in Breast Cancer

“…Thus, at least one marker was informative in 60% of cases. The heterozygosity rate of IDS was similar to what has been reported for the normal healthy Caucasian population (17); however, no data have been reported for G6PD in a normal healthy population. A representative data for IDS genotyping in 18 cases are shown in Fig.…”

Clonal analysis of TET2 and JAK2 mutations suggests that TET2 can be a late event in the progression of myeloproliferative neoplasms

“…Primers used for sequencing, copy number analysis, and X chromosomal inactivation analyses are provided in supplemental Table 1 (available on the Blood website; see the Supplemental Materials link at the top of the online article) and were performed as described. [17][18][19][20] …”

“…Accordingly, all colonies in this patient were positive for the TET2 mutation. The X-chromosome inactivation pattern in individual colonies from p226 with wild-type JAK2, as determined by scoring a C/T polymorphism in the 3Ј-untranslated region of the IDS mRNA, [18][19][20] revealed a strong skewing (10 of 10 expressed the C allele of IDS), indicating that these progenitors were of clonal origin ( Figure 1A). The finding of clonality suggests that this patient has a second significant disease clone, which does not carry a mutation in JAK2.…”

Mutations in the VHL gene in sporadic apparently congenital polycythemia

“…All 4 had polyclonal platelets and granulocytes (Table 1; a representative analysis is shown in Figure 4) indicating that their congenital polycythemia was due to germline mutation. 16,19 …”