Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

in Human Genomics (2023), 17(1), 39

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main ... [more ▼]

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques. [less ▲]

A performance-oriented comparative study of the Chapel high-productivity language to conventional programming environments

in PMAM '22: Proceedings of the Thirteenth International Workshop on Programming Models and Applications for Multicores and Manycores (2022, April 18)

The increase in complexity, diversity and scale of high performance computing environments, as well as the increasing sophistication of parallel applications and algorithms call for productivity-aware ... [more ▼]

The increase in complexity, diversity and scale of high performance computing environments, as well as the increasing sophistication of parallel applications and algorithms call for productivity-aware programming languages for high-performance computing. Among them, the Chapel programming language stands out as one of the more successful approaches based on the Partitioned Global Address Space programming model. Although Chapel is designed for productive parallel computing at scale, the question of its competitiveness with well-established conventional parallel programming environments arises. To this end, this work compares the performance of Chapel-based fractal generation on shared- and distributed-memory platforms with corresponding OpenMP and MPI+X implementations. The parallel computation of the Mandelbrot set is chosen as a test-case for its high degree of parallelism and its irregular workload. Experiments are performed on a cluster composed of 192 cores using the French national testbed Grid'5000. Chapel as well as its default tasking layer demonstrate high performance in shared-memory context, while Chapel competes with hybrid MPI+OpenMP in distributed-memory environment. [less ▲]

Ethical Concerns and Opportunities in Binding Intelligent Systems and Blockchain Technology

in Highlights in Practical Applications of Agents, Multi-Agent Systems and Trust-worthiness. The PAAMS Collection - International Workshops of PAAMS 2020, L'Aquila, Italy, October 7-9, 2020, Proceedings (2020)

The welfare impacts of an immigration amnesty: how drastic could they be?

Presentation (2016, September)

The Gain from the Drain: Welfare effects of Selective Migration

Presentation (2016, April)

Return Plans and Migrants' Behaviour

Presentation (2016, April)

The welfare impacts of an immigration amnesty: how drastic could they be?

Scientific Conference (2015, December 11)

Crise des réfugiés : quelques clarifications s'imposent !

Article for general public (2015)

Remittance and Migration Prospects for the Twenty-First Century

E-print/Working paper (2015)

Efficiency gains from liberalizing labor mobility

in Scandinavian Journal of Economics (2015), 117(2), 303-346

In this paper, we quantify the effect of a complete liberalization of cross-border migration on the world GDP and its distribution across regions. We build a general equilibrium model, endogenizing ... [more ▼]

In this paper, we quantify the effect of a complete liberalization of cross-border migration on the world GDP and its distribution across regions. We build a general equilibrium model, endogenizing bilateral migration and income disparities between and within countries. Our calibration strategy uses data on effective and potential migration to identify total migration costs and visa costs by education level. Data on potential migration reveal that the number of people in the world who have a desire to migrate is around 400 million. This number is much smaller than that predicted in previous studies, and reflects the existence of high “incompressible” migration costs. In our benchmark framework, liberalizing migration increases the world GDP by 11.5–12.5 percent in the medium term. Our robustness analysis reveals that the gains are always limited, in the range of 7.0 percent (with schooling externalities) to 17.9 percent (if network effects are accounted for). [less ▲]