Cell Line Controls for the Genotyping of a Spectrum of Human Single Nucleotide Polymorphisms in the Clinical Laboratory.

BACKGROUND: Genotyping for clinically important single nucleotide polymorphisms (SNPs) is performed by many clinical routine laboratories. To support testing, quality controls and reference materials are needed. Those may be derived from residual patient samples, left over samples of external quality assurance schemes, plasmid DNA or DNA from cell lines. DNAs from cell lines are commutable and available in large amounts. METHODS: DNA from 38 cell lines were examined for suitability as controls in 11 SNP assays that are frequently used in a clinical routine laboratory: FV (1691G>A), FII (20210G>A), PAI-1 4G/5G polymorphism, MTHFR (677C>T, 1298A>C), HFE (H63D, S65C, C282Y), APOE (E2, E3, E4), LPH (-13910C>T), UGT1A1 (*28, *36, *37), TPMT (*2, *3A, *3B, *3C), VKORC1 (-1639G>A, 1173C>T), CYP2C9 (*2, *3, *5). Genotyping was performed by real-time PCR with melting curve analysis and confirmed by bi-directional sequencing. RESULTS: We find an almost complete spectrum of genotypic constellations within these 38 cell lines. About 12 cell lines appear sufficient as genotypic controls for the 11 SNP assays by covering almost all of the genotypes. However, hetero- and homozygous genotypes for FII and the alleles TPMT*2, UGT1A1*37 and CYP2C9*5 were not detected in any of the cell lines. CONCLUSIONS: DNA from most of the examined cell lines appear suitable as quality controls for these SNP assays in the laboratory routine, as to the implementation of those assays or to prepare samples for quality assurance schemes. Our study may serve as a pilot to further characterize these cell lines to arrive at the status of reference materials.

Carbohydrate Malabsorption and Putative Carbohydrate-Specific Small Intestinal Bacterial Overgrowth: Prevalence and Diagnostic Overlap Observed in an Austrian Outpatient Center.

BACKGROUND/AIMS: While lactose malabsorption is a well-investigated condition, few epidemiologic data are available for fructose and sorbitol malabsorption. The aim of this study was to assess the prevalence rates for primary lactose malabsorption, fructose and sorbitol malabsorption, and carbohydrate-specific small intestinal bacterial overgrowth (cs-SIBO) in an Austrian outpatient center. METHODS: In total, 306 adult patients, who were primarily referred with suspected carbohydrate malabsorption by general practitioners to our outpatient clinic, underwent genetic testing (C/T-13910 polymorphism) for primary lactose malabsorption, and a combined hydrogen (H2)/methane (CH4) breath test for fructose (25 g) and sorbitol (12.5 g) malabsorption. Cohen's kappa (κ) was calculated for agreement between positive breath test results and self-reported symptoms during the test. RESULTS: Seventy-eight (25.49%) patients were C/C-13910 homozygotes, indicating primary lactose malabsorption. Thirty-four (11.11%) and 57 (18.63%) patients were classified as fructose and sorbitol malabsorbers. Cohen's κ measuring agreements between positive fructose and sorbitol breath test results and self-reported symptoms during the test were 0.33 and 0.49, respectively. Twenty-nine (9.50%) patients with an early H2/CH4 peak (i.e. within 60 minutes after fructose and/or sorbitol ingestion) were diagnosed with cs-SIBO. CONCLUSION: In Austria, carbohydrate malabsorption is a frequent condition in patients referred by general practitioners to carbohydrate malabsorption testing.

Assessment of human iron status: A cross-sectional study comparing the clinical utility of different laboratory biomarkers and definitions of iron deficiency in daily practice.

OBJECTIVES: No full international consensus exists on disease markers to be used for assessing the human iron status. Therefore this study was conducted to compare performances of serum ferritin and transferrin saturation (TSAT) versus soluble transferrin receptor (sTfR)/log ferritin and reticulocyte hemoglobin content (CHr), also known as Thomas-plot, in the diagnosis of iron deficiency (ID). DESIGN AND METHODS: A total of 445 consecutive hospitalized patients, referred for routine testing of the actual iron status, were included. Logistic regression models for the probability of functional ID (CHr<28pg) were constructed for all 445 patients, for 225 patients without (C-reactive protein [CRP]≤0.5mg/dL) and 220 patients with acute-phase reaction (CRP>0.5mg/dL). RESULTS: Based on the Thomas-plot analyses, 153/445 (34.38%) patients were identified with ID. When ID was diagnosed by means of serum ferritin levels<30ng/mL and TSAT levels<20%, 105/445 (23.60%) and 215/445 (48.31%) patients were identified with ID, respectively. The sTfR/log ferritin ratio showed the best positive predictive values (PPV) (62.50 and 64.41%) to indicate functional ID in patients without as well as with acute-phase reaction compared to sTfR (58.14 and 61.67%), ferritin (32.50 and 32.86%) and TSAT (26.74 and 42.86%). CONCLUSIONS: In clinical practice, the prevalence of ID and the accuracy to detect functional ID are dependent on marker selection and its definition. Regarding the results of this work, for laboratory investigation of ID, however, we suggest using Thomas-plot analyses in combination with ferritin single-marker measurements to efficiently identify patients with ID.

Hepcidin-25 vs. conventional clinical biomarkers in the diagnosis of functional iron deficiency.

OBJECTIVES: As hepcidin-25 is considered as a key regulator of human iron homoeostasis, this study aimed to compare this parameter with conventional biomarkers and diagnostic tools of iron deficiency (ID). METHODS: In total, 233 hospitalised adult patients, who underwent routine blood testing for ID, were included. All subjects were investigated for hepcidin-25, reticulocyte haemoglobin content (CHr), soluble transferrin receptor (sTfR)/log ferritin ratio (i.e. Thomas plot), sTfR, ferritin, transferrin saturation (TSAT), C-reactive protein (CRP) and for complete blood cell count. Functional ID was defined as a CHr < 28 pg. Separate logistic regression models were calculated with all potential biomarkers to evaluate and compare the predictive performance with respect to functional ID in patients without (CRP ≤ 0.5 mg/dL) and with (CRP > 0.5 mg/dL) acute-phase reaction, respectively. RESULTS: One hundred seventeen patients with CRP > 0.5 mg/dL showed a distinctly higher hepcidin-25 median value [35.60 (range: 4.27-80.03) ng/mL] as compared to 116 patients with CRP ≤ 0.5 mg/dL [18.55 (range: 3.77-73.01) ng/mL]. With respect to functional ID, sTfR/log ferritin ratio and sTfR were of better positive predictive value (PPV) (sTfR/log ferritin ratio: 58.33% and 70.83%; sTfR: 60.00% and 60.00%) than when compared to hepcidin-25 (PPV: 37.74% and 42.86%) and ferritin (PPV: 27.54% and 46.15%) in both subgroups. CONCLUSIONS: The sTfR/log ferritin ratio, as well as sTfR, were better predictors of functional ID in patients with and without acute-phase reaction as compared to hepcidin-25 and ferritin.