FPGA acceleration of DNA sequencing analysis and storage

In this work we explore how Field-Programmable Gate Arrays (FPGAs) can be used to alleviate the data processing bottlenecks in DNA sequencing. We focus our efforts on accelerating the FM-index, a data structure used to solve the computationally intensive string matching problems found in DNA sequencing analysis such as short read alignment. The main contributions of this work are: 1) We accelerate the FM-index using FPGAs and develop several novel methods for reducing the memory bottleneck of the search algorithm. These methods include customising the FM-index structure according to the memory architecture of the FPGA platform and minimising the number of memory accesses through both architectural and algorithmic optimisations. 2) We present a new approach for accelerating approximate string matching using the backtracking FM-index. This approach makes use of specialised approximate string matching modules and a run-time reconfigurable architecture in order to achieve both high sensitivity and high performance. 3) We extend the FM-index search algorithm for reference-based compression and accelerate it using FPGAs. This accelerated design is integrated into fastqZip and fastaZip, two new tools that we have developed for the fast and effective compression of sequence data stored in the FASTQ and FASTA formats respectively. We implement our designs on the Maxeler Max4 Platform and show that they are able to outperform state-of-the-art DNA sequencing analysis software. For instance, our hardware-accelerated compression tool for FASTQ data is able to achieve a higher compression ratio than the best performing tool, fastqz, whilst the average compression and decompression speeds are 25 and 43 times faster respectively.Open Acces

FPGA Acceleration of Reference-Based Compression for Genomic Data

Abstract-One of the key challenges facing genomics today is efficiently storing the massive amounts of data generated by nextgeneration sequencing platforms. Reference-based compression is a popular strategy for reducing the size of genomic data, whereby sequence information is encoded as a mapping to a known reference sequence. Determining the mapping is a computationally intensive problem, and is the bottleneck of most referencebased compression tools currently available. This paper presents the first FPGA acceleration of reference-based compression for genomic data. We develop a new mapping algorithm based on the FM-index search operation which includes optimisations targeting the compression ratio and speed. Our hardware design is implemented on a Maxeler MPC-X2000 node comprising 8 Altera Stratix V FPGAs. When evaluated against compression tools currently available, our tool achieves a superior compression ratio, compression time, and energy consumption for both FASTA and FASTQ formats. For example, our tool achieves a 30% higher compression ratio and is 71.9 times faster than the fastqz tool

Optimal timing of anticoagulation after acute ischemic stroke with atrial fibrillation (OPTIMAS) : Protocol for a randomized controlled trial

Rationale: Atrial fibrillation causes one-fifth of ischemic strokes, with a high risk of early recurrence. Although long-term anticoagulation is highly effective for stroke prevention in atrial fibrillation, initiation after stroke is usually delayed by concerns over intracranial hemorrhage risk. Direct oral anticoagulants offer a significantly lower risk of intracranial hemorrhage than other anticoagulants, potentially allowing earlier anticoagulation and prevention of recurrence, but the safety and efficacy of this approach has not been established. Aim: Optimal timing of anticoagulation after acute ischemic stroke with atrial fibrillation (OPTIMAS) will investigate whether early treatment with a direct oral anticoagulant, within four days of stroke onset, is as effective or better than delayed initiation, 7 to 14 days from onset, in atrial fibrillation patients with acute ischemic stroke. Methods and design: OPTIMAS is a multicenter randomized controlled trial with blinded outcome adjudication. Participants with acute ischemic stroke and atrial fibrillation eligible for anticoagulation with a direct oral anticoagulant are randomized 1:1 to early or delayed initiation. As of December 2021, 88 centers in the United Kingdom have opened. Study outcomes: The primary outcome is a composite of recurrent stroke (ischemic stroke or symptomatic intracranial hemorrhage) and systemic arterial embolism within 90 days. Secondary outcomes include major bleeding, functional status, anticoagulant adherence, quality of life, health and social care resource use, and length of hospital stay. Sample size target: A total of 3478 participants assuming event rates of 11.5% in the control arm and 8% in the intervention arm, 90% power and 5% alpha. We will follow a non-inferiority gatekeeper analysis approach with a non-inferiority margin of 2 percentage points. Discussion: OPTIMAS aims to provide high-quality evidence on the safety and efficacy of early direct oral anticoagulant initiation after atrial fibrillation-associated ischemic stroke. Trial registrations: ISRCTN: 17896007; ClinicalTrials.gov: NCT0375993

Optimal timing of anticoagulation after acute ischemic stroke with atrial fibrillation (OPTIMAS): Protocol for a randomized controlled trial

RATIONALE: Atrial fibrillation causes one-fifth of ischemic strokes, with a high risk of early recurrence. Although long-term anticoagulation is highly effective for stroke prevention in atrial fibrillation, initiation after stroke is usually delayed by concerns over intracranial hemorrhage risk. Direct oral anticoagulants offer a significantly lower risk of intracranial hemorrhage than other anticoagulants, potentially allowing earlier anticoagulation and prevention of recurrence, but the safety and efficacy of this approach has not been established. AIM: Optimal timing of anticoagulation after acute ischemic stroke with atrial fibrillation (OPTIMAS) will investigate whether early treatment with a direct oral anticoagulant, within four days of stroke onset, is as effective or better than delayed initiation, 7 to 14 days from onset, in atrial fibrillation patients with acute ischemic stroke. METHODS AND DESIGN: OPTIMAS is a multicenter randomized controlled trial with blinded outcome adjudication. Participants with acute ischemic stroke and atrial fibrillation eligible for anticoagulation with a direct oral anticoagulant are randomized 1:1 to early or delayed initiation. As of December 2021, 88 centers in the United Kingdom have opened. STUDY OUTCOMES: The primary outcome is a composite of recurrent stroke (ischemic stroke or symptomatic intracranial hemorrhage) and systemic arterial embolism within 90 days. Secondary outcomes include major bleeding, functional status, anticoagulant adherence, quality of life, health and social care resource use, and length of hospital stay. SAMPLE SIZE TARGET: A total of 3478 participants assuming event rates of 11.5% in the control arm and 8% in the intervention arm, 90% power and 5% alpha. We will follow a non-inferiority gatekeeper analysis approach with a non-inferiority margin of 2 percentage points. DISCUSSION: OPTIMAS aims to provide high-quality evidence on the safety and efficacy of early direct oral anticoagulant initiation after atrial fibrillation-associated ischemic stroke.Trial registrations: ISRCTN: 17896007; ClinicalTrials.gov: NCT03759938.This article is freely available online. Click on the 'Additional Link' above to access the full-text via the publisher's site.Published version, accepted version, submitted versio

The overlap between bronchiectasis and chronic airway diseases:state of the art and future directions

Bronchiectasis is a clinical and radiological diagnosis associated with cough, sputum production and recurrent respiratory infections. The clinical presentation inevitably overlaps with other respiratory disorders such as asthma and chronic obstructive pulmonary disease (COPD). In addition, 4-72% of patients with severe COPD are found to have radiological bronchiectasis on computed tomography, with similar frequencies (20-30%) now being reported in cohorts with severe or uncontrolled asthma. Co-diagnosis of bronchiectasis with another airway disease is associated with increased lung inflammation, frequent exacerbations, worse lung function and higher mortality. In addition, many patients with all three disorders have chronic rhinosinusitis and upper airway disease, resulting in a complex "mixed airway" phenotype.The management of asthma, bronchiectasis, COPD and upper airway diseases has traditionally been outlined in separate guidelines for each individual disorder. Recognition that the majority of patients have one or more overlapping pathologies requires that we re-evaluate how we treat airway disease. The concept of treatable traits promotes a holistic, pathophysiology-based approach to treatment rather than a syndromic approach and may be more appropriate for patients with overlapping features.Here, we review the current clinical definition, diagnosis, management and future directions for the overlap between bronchiectasis and other airway diseases