Early response to induction chemotherapy is an important prognostic factor in B-lymphoblastic leukemia (B-ALL). Here, we compare high-throughput sequencing (HTS) of and genes vs flow cytometry (FC) for measurable residual disease (MRD) detection at the end of induction chemotherapy in pediatric patients with newly diagnosed B-ALL. Six hundred nineteen paired pretreatment and end-of-induction bone marrow samples from Children's Oncology Group studies AALL0331 (clinicaltrials.gov #NCT00103285) (standard risk [SR]; with MRD by FC at any level) and AALL0232 (clinicaltrials.gov #NCT00075725) (high risk; with day 29 MRD <0.1% by FC) were evaluated by HTS and FC for event-free (EFS) and overall survival (OS). HTS and FC showed similar 5-year EFS and OS for MRD-positive and -negative patients using an MRD threshold of 0.01%. However, there was a high discordant rate with HTS identifying 55 (38.7%) more patients MRD positive at this threshold. These discrepant patients have worse outcomes than FC MRD-negative patients. In addition, the increased analytic sensitivity of HTS permitted identification of 19.9% of SR patients without MRD at any detectable level who had excellent 5-year EFS (98.1%) and OS (100%). The higher analytic sensitivity and lower false-negative rate of HTS improves upon FC for MRD detection in pediatric B-ALL by identifying a novel subset of patients at end of induction who are essentially cured using current chemotherapy and identifying MRD at 0.01% in up to one-third of patients who are missed at the same threshold by FC.

Purpose: Fragile X syndrome is caused by expansion and methylation of a CGG tract in the 5Ј untranslated region of the FMR1 gene. The estimated frequency of expanded alleles (Ն55 repeats) in the United States is 1:257-1:382, but these estimates were not calculated from unbiased populations. We sought to determine the frequency of fragile X syndrome premutation (55-200 repeats) and full mutation (Ͼ200 repeats) alleles in nonselected, unbiased populations undergoing routine carrier screening for other diseases. Methods: A previously validated laboratory-developed test using triplet-primed polymerase chain reaction was used to detect premutation and full mutation alleles in an unselected series of 11,759 consecutive cystic fibrosis carrier screening samples and 2011 samples submitted for screening for genetic diseases prevalent among the Ashkenazi Jewish population. Results: Premutations were identified in 48 cystic fibrosis screening samples (1:245) and 15 samples (1:134) from the Ashkenazi Jewish population. Adjusted for the ethnic mix of the US population and self-reported ethnicity in our screening population, the estimated female premutation carrier frequency in the United States was 1:178. The calculated frequency of full mutation alleles was 1:3335 overall, and the calculated premutation frequency in males was 1:400. Based on frequency of larger, Ն70 repeat alleles, and reported penetrance, the calculated fragile X-associated tremor and ataxia syndrome, and fragile X-associated primary ovarian insufficiency frequencies is 1:4848 and 1:3560, respectively. Conclusion: Our calculated fragile X syndrome carrier rate is higher than previous estimates for the US population and warrants further consideration of population-based carrier screening. Genet Med 2011:13(1): 39 -45.

Purpose:We sought to determine the genotype frequencies for cytochrome p450 enzyme 2C19 variant alleles both in the US panethnic population and various US ethnic groups and to establish the frequency of clinically actionable genotypes. methods:Analytical results were obtained from 1,396 consecutive samples submitted for cytochrome p450 enzyme 2C19 genotyping tests and stored in a proprietary database. This database was queried and genotypes and predicted phenotypes established. Anonymized samples were obtained from specimens submitted for cystic fibrosis genotyping that contained ethnicity information. Samples from 357, 149, and 346 individuals self-identified as white, African American, and Hispanic, respectively, were analyzed. In addition, 342 anonymized samples submitted for Ashkenazi Jewish panel testing were analyzed.Results: Significant ethnic differences were observed in the frequencies of the *17 ultrarapid allele among the various groups studied. In the pan-ethnic population, 3.8% of tested patients were classified as ultrarapid metabolizers, 24% as extensive metabolizers heterozygous for a *17 ultrarapid allele, 27% as intermediate metabolizers, and 3.5% as poor metabolizers. Using stringent criteria, 7.3% of individuals would have clinically actionable genotypes. In addition, we detected two individuals with a haplotype of *2/*17 and a single individual with a haplotype of *4/*17 indicating that the *17 hypermetabolic allele can occur on a *1, *2, or *4 background.Genet Med 2012:14(1):95-100

Purpose: To determine the accuracy of two commercially available kits for cystic fibrosis (CF) genotyping and determine allele frequencies for the ACMG/ACOG recommended mutations. Methods: A total of 1,040 consecutive analyses using Roche CF Gold Strips and the ABI CF Genotyper were performed. Subsequently we performed analyses of 20,103 samples. Results: Both kits accurately determined CF genotypes. The I148T mutation was found Ͼ100 times more frequently in carrier screening than in CF patients. Asymptomatic patients were identified who are compound heterozygotes for delta F508 and I148T. Four of 13 patients heterozygous for delta F508 and the IVS8-5T polymorphism had some symptoms of CF. Cystic fibrosis (CF) is one of the most common recessive genetic diseases in North America. In the March/April edition of this Journal, the Subcommittee on Cystic Fibrosis Screening of the American College of Medical Genetics (ACMG) published laboratory standards for population-based CF carrier screening. 1 The Committee recommended a core screening panel of 25 mutations with reflex testing under certain circumstances to four polymorphisms. These recommendations were based on the published frequencies of mutations observed in CF patients and other more subtle considerations such as a reluctance to screen for mutations causing congenital bilateral absence of the vas deferens (CBAVD). In October 2001, the American College of Obstetrics and Gynecology (ACOG) published its anticipated recommendation to College members to offer CF carrier detection to pregnant women. 2 In preparation for the release of the ACOG clinical practice guideline, we evaluated two of the commercially offered analytic platforms available as Analyte Specific Reagents (ASR) by performing blinded side by side analysis of 1,040 samples and determined that both performed acceptably.Our laboratory began screening for the College recommended panel in July 2001. To date, more than 20,000 samples have been analyzed. Many interesting observations are reported here with respect to test volumes, mutation frequencies, and accuracy of commercially available products. We also discuss clinical problems that have arisen. Our data and discussion provide insight into potential problems and solutions as CF population screening becomes integrated into standard obstetric care. MATERIALS AND METHODS Patient populationIn the period between July 1, 2001, and December 1, 2001, 20,103 consecutive samples submitted for CF DNA testing were analyzed for the ACMG recommended panel of mutations. Although information such as patient ethnicity and pertinent family history are requested for each patient, in practice, this information was only sporadically provided. When appropriate, physicians were contacted to obtain clinical information regarding patients with interesting genotypes. Because the indication was not routinely provided, we have no way to determine the number of tests performed for carrier detection versus mutation detection in a patient with CF, or infertility evaluations. The...

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