Newborn Screening Practices for Beta-Thalassemia in the United States.

Beta-thalassemia, a heritable condition of abnormal hemoglobin production, is not a core condition on the United States Recommended Uniform Screening Panel (RUSP) for state and territorial newborn screening (NBS) programs. However, screening for sickle cell disease (which is on the core RUSP) also detects reduced or absent levels of hemoglobin (Hb) A and certain other Hb variants associated with beta-thalassemia and, thus, allows for a timely referral to appropriate healthcare to minimize sequalae of the disease. The Association of Public Health Laboratories' Hemoglobinopathy Workgroup administered a comprehensive survey of all U.S. NBS programs to assess beta-thalassemia testing methodologies, the cutoffs for defining beta-thalassemia major, and the reporting and follow-up practices. Forty-six (87%) of the programs responded. Thirty-nine of the 46 responding programs (85%) report some form of suspected beta-thalassemia; however, the screening methods, the percentage of Hb A used as a cutoff for an indication of beta-thalassemia major, and the screening follow-up vary widely. The standardization of technical and reporting procedures may improve access to specialty care prior to severe complications, increase genetic counseling, and provide data needed to better understand the public health impact and clinical outcomes of beta-thalassemia in the United States.

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index.

Sequence-level searches on large collections of RNA sequencing experiments, such as the NCBI Sequence Read Archive (SRA), would enable one to ask many questions about the expression or variation of a given transcript in a population. Existing approaches, such as the sequence Bloom tree, suffer from fundamental limitations of the Bloom filter, resulting in slow build and query times, less-than-optimal space usage, and potentially large numbers of false-positives. This paper introduces Mantis, a space-efficient system that uses new data structures to index thousands of raw-read experiments and facilitates large-scale sequence searches. In our evaluation, index construction with Mantis is 6× faster and yields a 20% smaller index than the state-of-the-art split sequence Bloom tree (SSBT). For queries, Mantis is 6-108× faster than SSBT and has no false-positives or -negatives. For example, Mantis was able to search for all 200,400 known human transcripts in an index of 2,652 RNA sequencing experiments in 82 min; SSBT took close to 4 days.

Squeakr: an exact and approximate k-mer counting system.

Motivation: k-mer-based algorithms have become increasingly popular in the processing of high-throughput sequencing data. These algorithms span the gamut of the analysis pipeline from k-mer counting (e.g. for estimating assembly parameters), to error correction, genome and transcriptome assembly, and even transcript quantification. Yet, these tasks often use very different k-mer representations and data structures. In this article, we show how to build a k-mer-counting and multiset-representation system using the counting quotient filter, a feature-rich approximate membership query data structure. We introduce the k-mer-counting/querying system Squeakr (Simple Quotient filter-based Exact and Approximate Kmer Representation), which is based on the counting quotient filter. This off-the-shelf data structure turns out to be an efficient (approximate or exact) representation for sets or multisets of k-mers. Results: Squeakr takes 2×-4.3× less time than the state-of-the-art to count and perform a random-point-query workload. Squeakr is memory-efficient, consuming 1.5×-4.3× less memory than the state-of-the-art. It offers competitive counting performance. In fact, it is faster for larger k-mers, and answers point queries (i.e. queries for the abundance of a particular k-mer) over an order-of-magnitude faster than other systems. The Squeakr representation of the k-mer multiset turns out to be immediately useful for downstream processing (e.g. de Bruijn graph traversal) because it supports fast queries and dynamic k-mer insertion, deletion, and modification. Availability and implementation: https://github.com/splatlab/squeakr available under BSD 3-Clause License. Contact: ppandey@cs.stonybrook.edu. Supplementary information: Supplementary data are available at Bioinformatics online.

deBGR: an efficient and near-exact representation of the weighted de Bruijn graph.

MOTIVATION: Almost all de novo short-read genome and transcriptome assemblers start by building a representation of the de Bruijn Graph of the reads they are given as input. Even when other approaches are used for subsequent assembly (e.g. when one is using 'long read' technologies like those offered by PacBio or Oxford Nanopore), efficient k -mer processing is still crucial for accurate assembly, and state-of-the-art long-read error-correction methods use de Bruijn Graphs. Because of the centrality of de Bruijn Graphs, researchers have proposed numerous methods for representing de Bruijn Graphs compactly. Some of these proposals sacrifice accuracy to save space. Further, none of these methods store abundance information, i.e. the number of times that each k -mer occurs, which is key in transcriptome assemblers. RESULTS: We present a method for compactly representing the weighted de Bruijn Graph (i.e. with abundance information) with essentially no errors. Our representation yields zero errors while increasing the space requirements by less than 18-28% compared to the approximate de Bruijn graph representation in Squeakr. Our technique is based on a simple invariant that all weighted de Bruijn Graphs must satisfy, and hence is likely to be of general interest and applicable in most weighted de Bruijn Graph-based systems. AVAILABILITY AND IMPLEMENTATION: https://github.com/splatlab/debgr . CONTACT: rob.patro@cs.stonybrook.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Characterization of Deletions of the HBA and HBB Loci by Array Comparative Genomic Hybridization.

Thalassemia is among the most common genetic diseases worldwide. α-Thalassemia is usually caused by deletion of one or more of the duplicated HBA genes on chromosome 16. In contrast, most ß-thalassemia results from point mutations that decrease or eliminate expression of the HBB gene on chromosome 11. Deletions within the HBB locus result in thalassemia or hereditary persistence of fetal Hb. Although routine diagnostic testing cannot distinguish thalassemia deletions from point mutations, deletional hereditary persistence of fetal Hb is notable for having an elevated HbF level with a normal mean corpuscular volume. A small number of deletions accounts for most α-thalassemias; in contrast, there are no predominant HBB deletions causing ß-thalassemia. To facilitate the identification and characterization of deletions of the HBA and HBB globin loci, we performed array-based comparative genomic hybridization using a custom oligonucleotide microarray. We accurately mapped the breakpoints of known and previously uncharacterized HBB deletions defining previously uncharacterized deletion breakpoints by PCR amplification and sequencing. The array also successfully identified the common HBA deletions --(SEA) and --(FIL). In summary, comparative genomic hybridization can be used to characterize deletions of the HBA and HBB loci, allowing high-resolution characterization of novel deletions that are not readily detected by PCR-based methods.

DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements.

BACKGROUND: The brain, spinal cord, and neural retina comprise the central nervous system (CNS) of vertebrates. Understanding the regulatory mechanisms that underlie the enormous cell-type diversity of the CNS is a significant challenge. Whole-genome mapping of DNase I-hypersensitive sites (DHSs) has been used to identify cis-regulatory elements in many tissues. We have applied this approach to the mouse CNS, including developing and mature neural retina, whole brain, and two well-characterized brain regions, the cerebellum and the cerebral cortex. RESULTS: For the various regions and developmental stages of the CNS that we analyzed, there were approximately the same number of DHSs; however, there were many DHSs unique to each CNS region and developmental stage. Many of the DHSs are likely to mark enhancers that are specific to the specific CNS region and developmental stage. We validated the DNase I mapping approach for identification of CNS enhancers using the existing VISTA Browser database and with in vivo and in vitro electroporation of the retina. Analysis of transcription factor consensus sites within the DHSs shows distinct region-specific profiles of transcriptional regulators particular to each region. Clustering developmentally dynamic DHSs in the retina revealed enrichment of developmental stage-specific transcriptional regulators. Additionally, we found reporter gene activity in the retina driven from several previously uncharacterized regulatory elements surrounding the neurodevelopmental gene Otx2. Identification of DHSs shared between mouse and human showed region-specific differences in the evolution of cis-regulatory elements. CONCLUSIONS: Overall, our results demonstrate the potential of genome-wide DNase I mapping to cis-regulatory questions regarding the regional diversity within the CNS. These data represent an extensive catalogue of potential cis-regulatory elements within the CNS that display region and temporal specificity, as well as a set of DHSs common to CNS tissues. Further examination of evolutionary conservation of DHSs between CNS regions and different species may reveal important cis-regulatory elements in the evolution of the mammalian CNS.

Liver and heart MR relaxometry in iron loading: reproducibility of three methods.

PURPOSE: To compare the derived T2* values and reproducibility of three methods used to assess iron-loading in heart and liver. MATERIALS AND METHODS: In 23 pediatric patients, liver and cardiac gradient-echo imaging datasets (within-exam repeated sequence pairs) were evaluated. Data analyses compared derived relaxation values (average of pairs) and coefficient of variation (reproducibility of pairs). RESULTS: T2* values showed differences across methods, with pixel-wise mean > average fit > pixel-wise median. Coefficient of variation was found to be lower (better) with pixel-wise median and average fit methods compared to the pixel-wise mean technique. Maximum coefficient of variation values were lowest for the pixel-wise median approach in both the heart and liver. CONCLUSION: Differences in derived T2* values between methods must be considered when comparing values to established magnetic resonance imaging (MRI)-biopsy formulas. The pixel-wise median and average fit methods demonstrate substantial benefits in reproducibility compared to the pixel-wise mean method. Since minimal variation in measurement is critical for patient care, median processing of relaxometry data may be preferable in both tissue types.

A survey of perioperative management of sickle cell disease in North America.

BACKGROUND: Children with sickle cell disease frequently undergo surgical procedures that are associated with acute exacerbations of the disease. Current perioperative management practices are unclear. OBJECTIVES: We aimed at describing the current management. METHODS: We conducted an electronic survey of North American members of the Society for Pediatric Anesthesia, in which we asked about their perioperative management of sickle cell disease. RESULTS: The response rate to valid addresses was 25% (n=510/2006). In four scenarios, (a patient with mild disease undergoing a minor procedure; a patient with mild disease undergoing a more invasive procedure; a patient with severe disease undergoing a minor procedure; and a patient with severe disease undergoing a more invasive procedure) 80%, 38%, 27%, and 16% of respondents, respectively, would rely on oral fluids to hydrate patients during the preoperative fast, while 13%, 34%, 44%, and 59%, respectively, would use intravenous fluid. For the same four scenarios, 64%, 28%, 33%, and 10%, respectively, would not transfuse patients in an attempt to prevent sickle cell exacerbations, while 17%, 49%, 36%, and 51%, respectively, would transfuse to a hemoglobin concentration of 10 g·dl(-1). The tendencies to administer preoperative intravenous fluid and to transfuse blood increased with disease severity and procedure invasiveness (P<0.001). Although 89% felt comfortable managing patients with sickle cell disease, 73% thought an advisory statement on optimal perioperative management was needed. CONCLUSIONS: There is a wide variation in the management of children with sickle cell disease. Clinicians differentiate management based on disease severity and procedure type.