27 research outputs found
Methodology for Y Chromosome Capture: A complete genome sequence of Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads
This study is a comparison of the efficiency of three technologies used for Y chromosome capture and
the next-generation sequencing (NGS) technologies applied for determining its whole sequence. Our
main findings disclose that streptavidin–biotin magnetic particle-based capture methodology offers
better and a deeper sequence coverage for Y chromosome capture, compared to chromosome sorting
and microdissection procedures. Moreover, this methodology is less time consuming and the most
selective for capturing only Y chromosomal material, in contrast with other methodologies that result
in considerable background material from other, non-targeted chromosomes. NGS results compared
between two platforms, NextSeq 500 and SOLID 5500xl, produce the same coverage results. This is the
first study to explore a methodological comparison of Y chromosome capture and genetic analysis. Our
results indicate an improved strategy for Y chromosome research with applications in several scientific
fields where this chromosome plays an important role, such as forensics, medical sciences, molecular
anthropology and cancer sciences.Spanish Alfonso Martin Escudero Foundation for the financial support to one of the
authors of the present work (MJ Alvarez –Cubero)
Developing a utility index for the Aberrant Behavior Checklist (ABC-C) for fragile X syndrome
Purpose This study aimed to develop a utility index (the
ABC-UI) from the Aberrant Behavior Checklist-Community
(ABC-C), for use in quantifying the benefit of
emerging treatments for fragile X syndrome (FXS).
Methods The ABC-C is a proxy-completed assessment of
behaviour and is a widely used measure in FXS. A subset
of ABC-C items across seven dimensions was identified to
include in health state descriptions. This item reduction
process was based on item performance, factor analysis and
Rasch analysis performed on an observational study dataset,
and consultation with five clinical experts and a
methodological expert. Dimensions were combined into
health states using an orthogonal design and valued using
time trade-off (TTO), with lead-time TTO methods used
where TTO indicated a state valued as worse than dead.
Preference weights were estimated using mean, individual
level, ordinary least squares and random-effects maximum
likelihood estimation [RE (MLE)] regression models.
Results A representative sample of the UK general public
(n = 349; mean age 35.8 years, 58.2 % female) each valued
12 health states. Mean observed values ranged from
0.92 to 0.16 for best to worst health states. The RE (MLE)
model performed best based on number of significant
coefficients and mean absolute error of 0.018. Mean utilities
predicted by the model covered a similar range to that
observed.
Conclusions The ABC-UI estimates a wide range of
utilities from patient-level FXS ABC-C data, allowing
estimation of FXS health-related quality of life impact for
economic evaluation from an established FXS clinical trial
instrument
Evaluation of next-generation sequencing software in mapping and assembly
Next-generation high-throughput DNA sequencing technologies have advanced progressively in sequence-based genomic research and novel biological applications with the promise of sequencing DNA at unprecedented speed. These new non-Sanger-based technologies feature several advantages when compared with traditional sequencing methods in terms of higher sequencing speed, lower per run cost and higher accuracy. However, reads from next-generation sequencing (NGS) platforms, such as 454/Roche, ABI/SOLiD and Illumina/Solexa, are usually short, thereby restricting the applications of NGS platforms in genome assembly and annotation. We presented an overview of the challenges that these novel technologies meet and particularly illustrated various bioinformatics attempts on mapping and assembly for problem solving. We then compared the performance of several programs in these two fields, and further provided advices on selecting suitable tools for specific biological applications.published_or_final_versio