Richards, C. Sue

Abstract Background Noninvasive prenatal screening for common autosomal trisomies, sex chromosome aneuploidies and microdeletions vary by methodology and laboratory practice. The fetal portion of all cell-free DNA in the maternal circulation defines the fetal fraction (FF). The minimum specimen FF levels for reporting results vary between laboratories as well as the screening target (e.g., common trisomies vs select microdeletions). This variability can lead to confusion for both healthcare providers and patients. Methods Participants in the College of American Pathologists Non-Invasive Prenatal Testing 2021-B Exercise provided FF estimates for 3 manufactured samples. Responses to supplemental questions were also collected and analyzed. Results Overall, 72 of 77 participants responded. FF was measured by 66 participants using sequence counts (40), single nucleotide polymorphisms (15), fragment length (24), and Y chromosome sequences (24). Nearly half (48%) used multiple methods. For common trisomies, minimum FFs were none or <1% (n = 7), 1.0% to 3.9% (n = 35), 4.0% to 6.9% (n = 23), and ≥7.0% (n = 1); 4 participants did not measure FF. Challenge-specific FFs were variable with CVs of 13%, 15%, and 36%; the latter rate appears due to that sample’s fetal karyotype of 47,XYY. Comparing adjusted FF results for the 3 samples shows that 85% of participant results were within 20% of the consensus. Conclusions Using multiple methods to estimate FF was common, and cutoff levels for sample suitability varied widely. Within-laboratory FFs were less variable than between laboratories. Current FF estimates from clinical laboratories are not standardized and should be considered laboratory-specific.

Context.— Genomic reports are primarily organized in a narrative and unstructured format with variations in content and format. Regulatory requirements and professional guidelines for genetic test reporting exist but provide little guidance for effective communication of information. Objective.— To assess clinical genomic reporting practices across 5 disciplines within molecular diagnostics, including germline, somatic solid tumors, somatic hematologic malignancies, pharmacogenomics, and prenatal cell-free DNA screening. Design.— Reporting practices were assessed by using a structured review of clinical genomic reports from multiple laboratories in 5 molecular disciplines spanning different practice settings. Report content was reviewed by the presence/absence of from 27 to 44 elements, including 23 elements required by the College of American Pathologists and/or the Clinical Laboratory Improvement Amendments of 1988 (CLIA). If present, the element’s location on the report was recorded. Results.— A total of 69 genomics reports from 31 laboratories were reviewed. Overall, the reports were compliant with regulatory requirements but showed variability in both format and content. Six of 7 required reporting elements (per CLIA, 42 CFR [Code of Federal Regulations] 493.1291) were included in 90% of the reports. However, these elements were often located in different report sections. Only patient demographics were always found in a specific report section (header). Conclusions.— These results show that reports are overall compliant with regulatory requirements, despite some reporting elements being less consistently reported. The lack of consistent presentation of the data elements presents an opportunity to improve the communication of molecular testing results to clinicians and patients.

AbstractObjectiveDetermine current analytical methods and number of cell‐free (cf) DNA prenatal screening tests performed for common trisomies.MethodsThe College of American Pathologists 2022‐B Noninvasive Prenatal Testing exercise was distributed in December 2022 to 93 participants in 22 countries. Supplemental questions included the number of tests performed in a recent month and the proportion of samples originating outside the United States (US).ResultsEighty‐three participants from three continents returned results; 74 (89%) were suitable for the analyses. Nine manufacturer/platform combinations were identified, most commonly Illumina/Nextseq (55%). The most common methodology was whole genome sequencing (76%). Annualized cfDNA tests were 2.80 million, with Asian, European and North American participants representing 10.6%, 6.5% and 82.9% of tests, respectively. When restricted to US in‐country tests, the annualized rate was 2.18 million, with four of 20 participants testing 79.2%. Among 73 respondents, 63 (86%) were for‐profit, eight (11%) were non‐profit academic or government supported and the remaining two included hospital‐based and private non‐profit. Eighteen (25%) supported relevant academic training.ConclusionIn 2011, screening for common trisomies was based on serum/ultrasound markers with an estimated 2.96 million US pregnancies screened in 131 laboratories. In 2022, cfDNA‐based screening was offered by 20 laboratories testing 2.18 million US pregnancies.

Background: International guidelines recommend targeted screening to identify gestational thyroid dysfunction. However, currently used risk factors have questionable discriminative ability. We quantified the risk for thyroid function test abnormalities for a subset of risk factors currently used in international guidelines. Methods: We included prospective cohort studies with data on gestational maternal thyroid function and potential risk factors (maternal age, body mass index [BMI], parity, smoking status, pregnancy through in vitro fertilization, twin pregnancy, gestational age, maternal education, and thyroid peroxidase antibody [TPOAb] or thyroglobulin antibody [TgAb] positivity). Exclusion criteria were pre-existing thyroid disease and use of thyroid interfering medication. We analyzed individual participant data using mixed-effects regression models. Primary outcomes were overt and subclinical hypothyroidism and a treatment indication (defined as overt hypothyroidism, subclinical hypothyroidism with thyrotropin >10 mU/L, or subclinical hypothyroidism with TPOAb positivity). Results: The study population comprised 65,559 participants in 25 cohorts. The screening rate in cohorts using risk factors currently recommended (age >30 years, parity ≥2, BMI ≥40) was 58%, with a detection rate for overt and subclinical hypothyroidism of 59%. The absolute risk for overt or subclinical hypothyroidism varied <2% over the full range of age and BMI and for any parity. Receiver operating characteristic curves, fitted using maternal age, BMI, smoking status, parity, and gestational age at blood sampling as explanatory variables, yielded areas under the curve ranging from 0.58 to 0.63 for the primary outcomes. TPOAbs/TgAbs positivity was associated with overt hypothyroidism (approximate risk for antibody negativity 0.1%, isolated TgAb positivity 2.4%, isolated TPOAb positivity 3.8%, combined antibody positivity 7.0%; p < 0.001), subclinical hypothyroidism (risk for antibody negativity 2.2%, isolated TgAb positivity 8.1%, isolated TPOAb positivity 14.2%, combined antibody positivity 20.0%; p < 0.001) and a treatment indication (risk for antibody negativity 0.2%, isolated TgAb positivity 2.2%, isolated TPOAb positivity 3.0%, and combined antibody positivity 5.1%; p < 0.001). Twin pregnancy was associated with a higher risk of overt hyperthyroidism (5.6% vs. 0.7%; p < 0.001). Conclusions: The risk factors assessed in this study had poor predictive ability for detecting thyroid function test abnormalities, questioning their clinical usability for targeted screening. As expected, TPOAb positivity (used as a benchmark) was a relevant risk factor for (subclinical) hypothyroidism. These results provide insights into different risk factors for gestational thyroid dysfunction.

Abstract Context Interpretation of thyroid function tests during pregnancy is limited by the generalizability of reference intervals between cohorts due to inconsistent methodology. Objective (1) To provide an overview of published reference intervals for thyrotropin (TSH) and free thyroxine (FT4) in pregnancy, (2) to assess the consequences of common methodological between-study differences by combining raw data from different cohorts. Methods (1) Ovid MEDLINE, EMBASE, and Web of Science were searched until December 12, 2021. Studies were assessed in duplicate. (2) The individual participant data (IPD) meta-analysis was performed in participating cohorts in the Consortium on Thyroid and Pregnancy. Results (1) Large between-study methodological differences were identified, 11 of 102 included studies were in accordance with current guidelines; (2) 22 cohorts involving 63 198 participants were included in the meta-analysis. Not excluding thyroid peroxidase antibody–positive participants led to a rise in the upper limits of TSH in all cohorts, especially in the first (mean +17.4%; range +1.6 to +30.3%) and second trimester (mean +9.8%; range +0.6 to +32.3%). The use of the 95th percentile led to considerable changes in upper limits, varying from –10.8% to –21.8% for TSH and –1.2% to –13.2% for FT4. All other additional exclusion criteria changed reference interval cut-offs by a maximum of 3.5%. Applying these findings to the 102 studies included in the systematic review, 48 studies could be used in a clinical setting. Conclusion We provide an overview of clinically relevant reference intervals for TSH and FT4 in pregnancy. The results of the meta-analysis indicate that future studies can adopt a simplified study setup without additional exclusion criteria.

Abstract Context. —As part of a College of American Pathologists (CAP) proficiency testing survey, a comparison is made between human chorionic gonadotropin (hCG) results from an actual patient pool and a similarly targeted artificial sample. The goal is to gain insight into the possible source(s) of bias attributable to the proficiency testing material (PTM) with a view toward creating more appropriate survey materials. Objective. —To compare hCG and related variants in a pool of fresh frozen sera (FFS) with that found in PTM. Design. —The 2003 CAP K/KN-A Survey included a FFS specimen along with admixtures of PTM. The FFS (K-02) and 1 PTM admixture (K-01) had similar mean hCG values. Five hCG-related analytes were measured on these 2 samples by a reference laboratory. Participants. —Approximately 1800 clinical laboratories and diagnostic test kit manufacturers participated in the K/ KN-A Survey. Main Outcome Measures. —Method imprecision (coefficient of variation) and method bias (relative difference between peer group mean and all-method median) were computed for the 2 samples. Differences were evaluated with respect to hCG-related analytes levels. Results. —All-method hCG results were 12.9 mIU/mL (12.9 IU/L) for the PTM material and 21.6 mIU/mL (21.6 IU/L) for the FFS material. Method biases for 14 manufacturers were greater for PTM than for FFS (−40% to +35% and −16% to +23%). Twelve of 14 methods had higher coefficients of variation on PTM. Total hCG and free β hCG measurements by the reference laboratory were 14.1 mIU/ mL (14.1 IU/L) for the PTM material and 18.5 mIU/mL (18.5 U/L) for the FFS material (FFS), and 2.4 (PTM) and 0.7 (FFS) mIU/mL (2.4 and 0.7 IU/L), respectively. On a molar basis, free β represented 17% and 4% of the total hCG, respectively. Levels of hyperglycosylated hCG, nicked hCG, and β core fragment were not measurable in either sample. Conclusions. —It is unlikely that the hCG added to the PTM is the source of the increased bias and variability. The main difference is a 3-fold increase in free β found in the PTM, but methods previously found to strongly react with free β were not systematically elevated. The biases between manufacturers found for the FFS specimen are likely attributable to calibration differences.

Abstract Objective.—To determine if the levels of imprecision of the commonly used analytic methods for drug measurements are suitable for long-term therapeutic drug monitoring. Design.—In 1996, 4 identical lyophilized samples (2 in the first mailing and 2 in the second mailing 4 months later) were sent to laboratories participating in a nationwide proficiency testing program. Similarly, in 1999, replicates from a liquid pool of spiked sera were mailed 3 times, 4 months apart, to participating laboratories. For each of 11 drugs regulated under the Clinical Laboratory Improvement Amendments of 1988 and 1 metabolite, the total variance for each method was partitioned into within- and between-laboratory components. The total within-laboratory and the total survey coefficients of variation (CVs) for each method were then compared with the “acceptable” precision criteria of Glick, Burnett, and Fraser for each drug. Setting.—The first 2 mailings of the College of American Pathologists Therapeutic Drug Monitoring surveys for 1996, sets Z and ZM, and the 3 mailings of 1999, sets ZM, Z, and Z2. Main Outcome Measures.—For each drug studied, the CV of each method was compared with the various imprecision criteria, and if greater than any of the criteria, the method was then tabulated as not meeting that specific criterion. Participants.—The approximately 5000 participants of the survey. Results.—The number of methods deemed as not having acceptable total long-term within-laboratory precision by the various criteria ranged from 35% to 88% in 1996 and from 22% to 77% in 1999. Conclusion.—The number of failures possibly indicates that many of the reagent assays being utilized are not precise enough for long-term therapeutic drug monitoring of chronically administered drugs or that the published criteria used to evaluate the data in this study are too stringent.

Abstract Objective. —To determine the magnitudes and sources of analytic variation in testing for therapeutic drugs. Specifically, among laboratories using the same analytic method, to compare the within-laboratory variation (including both short- and long-term variation) with the between-laboratory variation. Design. —Four identical challenges were prepared from a lyophilized pool of spiked sera and were sent in pairs 4 months apart to laboratories participating in a nationwide proficiency-testing program. For each of 25 drugs, the variability in reported results from laboratories using the same method was investigated using nested analysis of variance. Setting. —The first 2 mailings of the College of American Pathologists Therapeutic Drug Monitoring Survey, 1996, sets Z and ZM. Main Outcome Measures. —For each drug, total variance was partitioned into within- and between-laboratory components for common methods. The within-laboratory component was further partitioned into short- and long-term components. Participants. —The approximately 5000 laboratories enrolled in the survey. Results. —For the 25 drugs, the average percentages of the total variance due to short-term, within-laboratory variance; long-term, within-laboratory variance; between-laboratory variance; and total laboratory variance were 25.0% (range, 8.8–50.6%), 57.8% (35.3–73.7%), 17.3% (5.0–35.4%), and 82.7% (64.6–95.0%), respectively. Conclusion. —For all drugs tested, the within-laboratory component of variance was greater than the between-laboratory component of variance. Within laboratories, the magnitude of the long-term component was generally greater than the magnitude of the short-term component. This information will be helpful in determining the clinical utility of various drug assays and in evaluating the appropriateness of regulations involving therapeutic drug testing.