The value of DNA storage and pedigree analysis in rare diseases: a 17-year-old boy with X-linked lymphoproliferative disease (XLP) caused by a de novo SH2D1A mutation

Variation among DNA banking consent forms: points for clinicians to bank on

Deoxyribonucleic acid (DNA) banking is an important laboratory service that preserves the option of future genetic testing. DNA bank consent forms are a critical tool to facilitate thorough and valid informed consent. The objectives of this study were to assess the level of consistency of current clinical DNA banking consent forms with the American Society of Human Genetics (ASHG) and the American College of Medical Genetics and Genomics (ACMG) guidance and to explore variation among the forms. The content analysis matrix included key points identified from the ASHG and ACMG documents (including benefits/risks, sample storage, access, disposition, and communication) and additional points beyond the ASHG and ACMG documents identified from the consent forms themselves during the analysis process. Forms were assessed for language addressing each point. Five consent forms were identified and analyzed for twelve key points and eight additional points. The average consistency for key points was 10.8/12 (range 8/12 to 12/12). The range for additional points was 1/8 to 5/8. There was variation across forms in the details provided related to key and additional points. Gaps in clinical DNA banking consent forms are barriers to achieving informed consent. Clinicians can consider the consent key and additional points discussed here to supplement and enrich their clinical DNA banking informed consent discussions, promote stewardship, and maximize downstream utility of banked DNA. The identification of multiple additional points beyond the ASHG and ACMG documents' key points indicates a need for this guidance to be updated.

Demographic and socioeconomic trends in DNA banking utilization in the USA

Demographic and clinical information from de-identified individuals utilizing a single DNA banking service over a 22-year period was assessed using descriptive statistics. The socioeconomic characteristics of the study population were estimated using a zip code–level analysis of US Census data and compared to national US Metrics for 2016. Samples from 4,874 individuals were deposited to a single commercial DNA bank from 1997 to 2019. Samples originated from 31 countries across 6 continents, with the majority of samples originating from the United States (US; 97.37%; n = 4,746). A higher proportion of individuals identifying as females (55.58%; n = 2,709) utilized the service compared to males (41.18%; n = 2,007). The age distribution was bimodal, peaking around 5 years of age and again around 65 years of age. Whole blood was the preferred specimen for submission. Sample deposits peaked in 2015 with 559 annual deposits. Clinical genetic counselors were the most common referral source (41.73%; n = 2,034). Individuals utilizing DNA banking services are estimated to reside in wealthier, more educated and less racially diverse zip codes compared to national metrics. Although direct to consumer DNA banking is being utilized by the general public and clinical genetic counselors in the US, it is not widespread.

Novel Mutations in SH2D1A Gene in X-linked Lymphoproliferative Syndrome, Diagnosed After B-Cell Non-Hodgkin Lymphoma

BACKGROUND

X-linked lymphoproliferative disease type I (XLP I) is caused by mutations in the SH2D1A gene and characterized mainly by hypogammaglobulinemia and abnormal response to Epstein-Barr virus with a high predisposition to B-cell non-Hodgkin lymphoma development.

OBSERVATIONS

In this article, we describe the experience of 2 centers in Belarus and in Russia that follow 3 male patients who were diagnosed with XLP I after lymphoma development and treatment. Three novel mutations c.51G>C (p.E17D), c.192G>T (p.W64C), and c.53insA (p.K18KfsX67) were found in 3 males patients with XLP I. Two of them did not have any signs of immunodeficiency before B-cell non-Hodgkin lymphoma development.

CONCLUSIONS

We propose SH2D1A mutational screening be considered in male patients with or without hypogammaglobulinemia who received rituximab treatment for lymphoma and did not recover immunoglobulin G in a year after B-depleting therapy.

Comparison of Th1/Th2 cytokine profiles between primary and secondary haemophagocytic lymphohistiocytosis

Background

Haemophagocytic lymphohistiocytosis (HLH) is a life-threatening disorder of immune regulation, and HLH patients with mutations in genes including PRF1, UNC13D, STX11, STXBP2, SH2D1A, XIAP, and ITK were reported to be primary HLH. Due to the different treatment options, the differentiation between primary and secondary HLH is critical. Our previous studies have showed that a Th1/Th2 cytokine profile is diagnostic for HLH, yet the cytokine profiles between primary and secondary HLH have not been compared. The aim of the study was to test whether the Th1/Th2 cytokine profile could be used as a tool to differentiate between primary and secondary HLH.

Methods

A total of 45 hospitalized Chinese children with HLH during the period of February 2010 through September 2012 were enrolled in the study. Fifty healthy children were enrolled as controls. Primary HLH related genes were sequenced using genomic DNA samples. The Th1/Th2 cytokine levels including interferon-γ (IFN-γ), tumor necrosis factor-alpha (TNF-α), interleukin (IL)-10, IL-6, IL-4 and IL-2 were quantitatively determined by cytometric bead assay techniques.

Results

Primary HLH group (n = 4) included one patient with biallelic heterozygous mutations in PRF1 gene, and three patients with hemizygous mutation in SH2D1A gene. Based on the available genetic data, the other 41 patients were classified into the secondary HLH group. When compared the cytokine levels between the two groups, IL-4 level in primary-HLH was significantly lower than that in secondary HLH (P = 0.025), while IFN-γ level in primary HLH had a tendency of statistically lower than that in secondary HLH (P = 0.051). Area under receiver operating characteristic (ROC) curves of IL-4 and IFN-γ, IL-10, TNF-α, IL-2, and IL-6 levels were 0.841, 0.799, 0.506, 0.494, 0.457, and 0.250, respectively. ROC curves showed that 1.7 pg/ml of IL-4 had sensitivity and specificity for differentiation between primary and secondary HLH as 70.7 and 100.0 %, while 433.9 pg/ml of IFN-γ had sensitivity and specificity as 51.2 and 100.0 %, respectively.

Conclusions

HLH patients with lower IL-4 and IFN-γ levels have higher possibility to be primary HLH. The cytokine profile may be used as an additional tool for the quick differential diagnosis between primary and secondary HLH.

Electronic supplementary material

The online version of this article (doi:10.1186/s13052-016-0262-7) contains supplementary material, which is available to authorized users.

Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability

Whole-genome microarray analysis is proven to be useful in the identification of submicroscopic copy number imbalances in families with intellectual disabilities. The first case of Xq25 duplication was identified using genome-wide array comparative genomic hybridization (array-CGH) in a 24-year-old patient with a syndromic intellectual disability. We report a 4-year-old boy with a de novo 591 kb duplication at Xq25. The duplication was first detected by a CytoScan HD array platform (Affymetrix, USA) and was confirmed by real-time quantitative PCR (qPCR) of the STAG2 gene, and by fluorescence in situ hybridization (FISH). The patient had clinical features partially consistent with published cases, including an intellectual disability and speech delay. The identification of this additional patient and a detailed analysis of duplications identified in other patient cohorts and absent in normal individuals support the existence of a rare pathological microduplication at Xq25 that encompasses STAG2.