Hamza N. Khan

Detection of static cyclotorsion and compensation for dynamic cyclotorsion in laser in situ keratomileusis

PURPOSE: To evaluate the degree of static and dynamic cyclotorsion using a rotational eye tracker in laser in situ keratomileusis (LASIK) to correct myopic astigmatism. SETTING: Rothschild Foundation, Paris, France. DESIGN: Cohort study. METHODS: Laser in situ keratomileusis with active iris registration using a Zyoptix 100 Hz excimer laser with Advanced Control Eyetracking was performed in eyes with myopic astigmatism. In all cases, iris registration was used to evaluate the degree of static cyclotorsion preoperatively and the degree of dynamic cyclotorsion and intraoperatively. The direction, mean values, and ranges of static and dynamic cyclotorsion were recorded. The amplitude of intraoperative cyclotorsion was reported. RESULTS: The study included 74 consecutive eyes (38 patients). The direction of cyclotorsion was not statistically significant. The mean static cyclotorsion was 3.08 degrees ± 2.68 (SD) (range −7.0 to 14.0 degrees) and the mean dynamic cyclotorsion, 3.39 ± 2.94 degrees (range −10.3 to 13.5 degrees). During photoablation, the mean amplitude of cyclotorsion was 2.69 ± 1.63 degrees (range 0.0 to 9.2 degrees). The magnitude of dynamic cyclotorsion was less than 5 degrees in 66% of eyes, 5 degrees or more in 34% of eyes, and 10 degrees or more in 4% of eyes. CONCLUSIONS: Static and dynamic cyclotorsion was detected with a dynamic eye tracker in eyes having LASIK. Rotational movements were mainly static but had significant amplitude during photoablation. Financial Disclosure: No author has a financial or proprietary interest in any material or method mentioned.

The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA

Frogs play important ecological roles, and several species are important model organisms for scientific research. The globally distributed Ranidae (true frogs) are the largest frog family, and have substantial evolutionary distance from the model laboratory Xenopus frog species. Unfortunately, there are currently no genomic resources for the former, important group of amphibians. More widely applicable amphibian genomic data is urgently needed as more than two-thirds of known species are currently threatened or are undergoing population declines. We report a 5.8 Gbp (NG50 = 69 kbp) genome assembly of a representative North American bullfrog (Rana [Lithobates] catesbeiana). The genome contains over 22,000 predicted protein-coding genes and 6,223 candidate long noncoding RNAs (lncRNAs). RNA-Seq experiments show thyroid hormone causes widespread transcriptional change among protein-coding and putative lncRNA genes. This initial bullfrog draft genome will serve as a key resource with broad utility including amphibian research, developmental biology, and environmental research.The globally-distributed Ranidae (true frogs) are the largest frog family. Here, Hammond et al. present a draft genome of the North American bullfrog, Rana (Lithobates) catesbeiana, as a foundation for future understanding of true frog genetics as amphibian species face difficult environmental challenges.

ntCard: A streaming algorithm for cardinality estimation in genomics data

Motivation: Many bioinformatics algorithms are designed for the analysis of sequences of some uniform length, conventionally referred to as k‐mers. These include de Bruijn graph assembly methods and sequence alignment tools. An efficient algorithm to enumerate the number of unique k‐mers, or even better, to build a histogram of k‐mer frequencies would be desirable for these tools and their downstream analysis pipelines. Among other applications, estimated frequencies can be used to predict genome sizes, measure sequencing error rates, and tune runtime parameters for analysis tools. However, calculating a k‐mer histogram from large volumes of sequencing data is a challenging task. Results: Here, we present ntCard, a streaming algorithm for estimating the frequencies of k‐mers in genomics datasets. At its core, ntCard uses the ntHash algorithm to efficiently compute hash values for streamed sequences. It then samples the calculated hash values to build a reduced representation multiplicity table describing the sample distribution. Finally, it uses a statistical model to reconstruct the population distribution from the sample distribution. We have compared the performance of ntCard and other cardinality estimation algorithms. We used three datasets of 480 GB, 500 GB and 2.4 TB in size, where the first two representing whole genome shotgun sequencing experiments on the human genome and the last one on the white spruce genome. Results show ntCard estimates k‐mer coverage frequencies >15× faster than the state‐of‐the‐art algorithms, using similar amount of memory, and with higher accuracy rates. Thus, our benchmarks demonstrate ntCard as a potentially enabling technology for large‐scale genomics applications. Availability and Implementation: ntCard is written in C ++ and is released under the GPL license. It is freely available at https://github.com/bcgsc/ntCard. Contact: hmohamadi@bcgsc.ca or ibirol@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online.Abstract Motivation Many bioinformatics algorithms are designed for the analysis of sequences of some uniform length, conventionally referred to as k-mers. These include de Bruijn graph assembly methods and sequence alignment tools. An efficient algorithm to enumerate the number of unique k-mers, or even better, to build a histogram of k-mer frequencies would be desirable for these tools and their downstream analysis pipelines. Among other applications, estimated frequencies can be used to predict genome sizes, measure sequencing error rates, and tune runtime parameters for analysis tools. However, calculating a k-mer histogram from large volumes of sequencing data is a challenging task. Results Here, we present ntCard, a streaming algorithm for estimating the frequencies of k-mers in genomics datasets. At its core, ntCard uses the ntHash algorithm to efficiently compute hash values for streamed sequences. It then samples the calculated hash values to build a reduced representation multiplicity table describing the sample distribution. Finally, it uses a statistical model to reconstruct the population distribution from the sample distribution. We have compared the performance of ntCard and other cardinality estimation algorithms. We used three datasets of 480 GB, 500 GB and 2.4 TB in size, where the first two representing whole genome shotgun sequencing experiments on the human genome and the last one on the white spruce genome. Results show ntCard estimates k-mer coverage frequencies >15× faster than the state-of-the-art algorithms, using similar amount of memory, and with higher accuracy rates. Thus, our benchmarks demonstrate ntCard as a potentially enabling technology for large-scale genomics applications. Availability and Implementation ntCard is written in C ++ and is released under the GPL license. It is freely available at https://github.com/bcgsc/ntCard. Supplementary information Supplementary data are available at Bioinformatics online.

It′s okay to be green: Draft genome of the North American Bullfrog (Rana [Lithobates] catesbeiana)

Frogs play important ecological roles as sentinels, insect control and food sources. Several species are important model organisms for scientific research to study embryogenesis, development, immune function, and endocrine signaling. The globally-distributed Ranidae (true frogs) are the largest frog family, and have substantial evolutionary distance from the model laboratory Xenopus frog species. Consequently, the extensive Xenopus genomic resources are of limited utility for Ranids and related frog species. More widely applicable amphibian genomic data is urgently needed as more than two-thirds of known species are currently threatened or are undergoing population declines. Herein, we report on the first genome sequence of a Ranid species, an adult male North American bullfrog (Rana [Lithobates] catesbeiana). We assembled high-depth Illumina reads (66-fold coverage), into a 5.8 Gbp (NG50 = 57.7 kbp) draft genome using ABySS v1.9.0. The assembly was scaffolded with LINKS and RAILS using pseudo-long-reads from targeted denovo assembler Kollector and Illumina Synthetic Long-Reads, as well as reads from long fragment (MPET) libraries. We predicted over 22,000 protein-coding genes using the MAKER2 pipeline and identified the genomic loci of 6,227 candidate long noncoding RNAs (IncRNAs) from a composite reference bullfrog transcriptome. Mitochondrial sequence analysis supported Lithobates as a subgenus of Rana. RNA-Seq experiments identified ~6,000 thyroid hormone– responsive transcripts in the back skin of premetamorphic tadpoles; the majority of which regulate DNA/RNA processing. Moreover, 1/6th of differentially-expressed transcripts were putative lncRNAs. Our draft bullfrog genome will serve as a useful resource for the amphibian research community.

Use of Toric IOLs in the Correction of Astigmatism with Cataract Surgery

Toric IOLS provide a safe and effective means of correcting astigmatism at the time of cataract surgery. Little additional risk is involved. Careful surgical planning involves precise preoperative evaluation of the ocular surface, refractive characteristics, and the use of alignment systems. Improvements in IOL design and materials have reduced the need for postoperative enhancements due to IOL rotation. Alignment remains an area of rapid technologic development with intraoperative guidance using microscope-integrated or “heads-up” displays becoming available.

Ten Key Points to Optimize Surgical Correction of Astigmatism

Preoperative measurements of corneal astigmatism need to be sufficiently accurate to reduce preexisting astigmatism to within 0.50 (multifocal IOLs)–0.75 D (monofocal IOLs). Our diagnostic tools include manual or autokeratometers, optical biometry, and, importantly, topography or tomography. A prerequisite condition to guarantee the quality of the measurements is a healthy cornea, without any surface irregularities caused by either deficient tear film or corneal pathology: Corneal astigmatism can be identified with manual and autokeratometers in a repeatable manner. However, these instruments are insufficient because they only measure four points in the central 3 mm of the cornea and are unable to detect astigmatic asymmetries, irregularities, posterior corneal, nor lenticular astigmatism. Optical biometry provides magnitude and axis measurements at various optical zones (1.65, 2.3, or 3.3 mm depending on the instrument) with variable numbers of points (6, 18, and 32). Corneal topography has become a mandatory test prior to toric implantation as it allows for the detection of asymmetric and irregular astigmatism. Comparative studies between manual and automated keratometry, Placido-type topography, and simulated keratometry of Scheimpflug systems showed similar results in terms of anterior corneal magnitude, but axis differences were noted [1–3]. Corneal topographers may usually be considered as the final judge in terms of axis, pending verification of the image quality. Total corneal astigmatism includes anterior and posterior components of the cylinder. Previous methods measured the anterior component only, whereas slit-scanning technology, optical coherence tomography, and Scheimpflug imaging systems allow for the measurement of both anterior and posterior astigmatism. These newer systems use true refractive indices to calculate the anterior and posterior corneal powers (1.376 for the cornea and 1.336 for the aqueous), instead of a standardized corneal refractive index of 1.3375 [4]. Accuracy is still suboptimal, but these devices hold the promise that they can be used to reliably measure posterior astigmatism and optimize the estimation of total corneal astigmatism.

Excimer Laser Correction of Astigmatism: Principles and Clinical Results

Excimer laser photorefractive keratectomy (PRK) was first introduced by Trokel in 1983 to correct myopia [1]. Seiler and coauthors in 1988 proposed this technology to correct astigmatism with T cuts, but the refractive results were not superior to incisional techniques [2]. In 1991, McDonnell published promising clinical results with photoastigmatic refractive keratectomy (PARK) using toric ablation [3]. Since then, more than 20 million excimer laser procedures have been performed, and this technology has become the method of choice to correct both spherical and astigmatic errors. As a result, corneal refractive surgery is the second most frequently performed ocular procedure worldwide, just after cataract surgery.

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data

Motivation: Sequencing studies on non‐model organisms often interrogate both genomes and transcriptomes with massive amounts of short sequences. Such studies require de novo analysis tools and techniques, when the species and closely related species lack high quality reference resources. For certain applications such as de novo annotation, information on putative exons and alternative splicing may be desirable. Results: Here we present ChopStitch, a new method for finding putative exons de novo and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon‐exon boundaries in de novo assembled RNA‐Seq data with the help of a Bloom filter that represents the k‐mer spectrum of WGSS reads. The algorithm also accounts for base substitutions in transcript sequences that may be derived from sequencing or assembly errors, haplotype variations, or putative RNA editing events. The primary output of our tool is a FASTA file containing putative exons. Further, exon edges are interrogated for alternative exon‐exon boundaries to detect transcript isoforms, which are represented as splice graphs in DOT output format. Availability and implementation: ChopStitch is written in Python and C++ and is released under the GPL license. It is freely available at https://github.com/bcgsc/ChopStitch. Contact: hkhan@bcgsc.ca or ibirol@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online.

Correction of High Astigmatism: Case Studies Using the Mixed-cylinder Approach

PURPOSE To explain the use of the mixed-cylinder approach in treating moderate to high astigmatism with the NIDEK EC-5000 excimer laser system. METHODS Retrospective case series report. RESULTS Three patients with bilateral moderate to high astigmatism were treated successfully using the mixed cylinder approach. CONCLUSIONS The use of the mixed-cylinder approach with the NIDEK EC-5000 excimer laser may be a safe and predictable option for treating moderate to high astigmatism.