PubMed Highlight: A Refreshing Pineapple Juice!

Do you like a sweet refreshing pineapple juice in a hot summer afternoon? Sure I do! And now there are hope that this juice would become even better! The full trascriptome of Pineapple as just been released and described in this paper published on PLOS ONE, so that genetic selection could applied to improve the fruit and the juice!

De Novo Assembly, Characterization and Functional Annotation of Pineapple Fruit Transcriptome through Massively Parallel Sequencing
Wen Dee Ong, Lok-Yung Christopher Voo, Vijay Subbiah Kumar
Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia

Abstract

Background
Pineapple (Ananas comosus var. comosus), is an important tropical non-climacteric fruit with high commercial potential. Understanding the mechanism and processes underlying fruit ripening would enable scientists to enhance the improvement of quality traits such as, flavor, texture, appearance and fruit sweetness. Although, the pineapple is an important fruit, there is insufficient transcriptomic or genomic information that is available in public databases. Application of high throughput transcriptome sequencing to profile the pineapple fruit transcripts is therefore needed.

Methodology/Principal Findings
To facilitate this, we have performed transcriptome sequencing of ripe yellow pineapple fruit flesh using Illumina technology. About 4.7 millions Illumina paired-end reads were generated and assembled using the Velvet de novo assembler. The assembly produced 28,728 unique transcripts with a mean length of approximately 200 bp. Sequence similarity search against non-redundant NCBI database identified a total of 16,932 unique transcripts (58.93%) with significant hits. Out of these, 15,507 unique transcripts were assigned to gene ontology terms. Functional annotation against Kyoto Encyclopedia of Genes and Genomes pathway database identified 13,598 unique transcripts (47.33%) which were mapped to 126 pathways. The assembly revealed many transcripts that were previously unknown.

Conclusions
The unique transcripts derived from this work have rapidly increased of the number of the pineapple fruit mRNA transcripts as it is now available in public databases. This information can be further utilized in gene expression, genomics and other functional genomics studies in pineapple.

BGI Workshop in Milan, Italy (December 5, 2012)

The Translational Science of Mendelian Disorders: From transomics to daily life

Wednesday, December 5, 2012 from 9:00 AM to 6:00 PM (PST), Milan, Italy

About the workshop

The aim of this workshop is to exchange ideas and discuss cutting-edge research in the field of Mendelian Disorder by bringing together scientists from all around Europe and even the world. Our workshop will be a forward thinking platform that aids our participants to review the specific topics, as well as to discuss future research.
We except to have 150-200 high ranked participants who are the top researchers from leading European research centers, universities as well as government representatives. These scientific researchers would come from Italy, Switzerland, France and other countries around.

The Program

Contact Information:

Ms Wenyan Li, Project Coordinator of Italy, BGI Europe
liwenyan@genomics.org.cn
+39 3313812359

Ms Mingyu Tian, Project Coordinator of Italy, BGI Europe
tianmingyu@genomics.org.cn
+39 3426496811

Online Registration:

http://bgi-workshop-srch.eventbrite.com

NGS PubMed Highlights: Human Molecular Genetics "Genomic Medicine" Issue

Human Molecular Genetics has published its latest review issue, featuring invited articles from top researchers in the field of Genomic Medicine.

Flash Report: Beer genome sequenced

Actually is the barley genome that has been sequenced and described in the journal Nature by scientists of The International Barley Sequencing Consortium (IBSC).
Malted barley, along with hops and yeast, is a key ingredient in brewing beer (while the yeast genome has been unraveled more than 15 years ago, to the best of my knowledge the hops - Humulus lupulus - genome has not been sequenced yet).
First cultivated more than 10,000 years ago, barley (Hordeum vulgare) is the world's fourth most important cereal crop (both in terms of area of cultivation and in quantity of grain produced), trailing only maize, rice and wheat. Its genome is almost twice the size of the human genome and contains a large proportion of closely related sequences, which are difficult to piece together.

Professor Robbie Waugh (Scotland's James Hutton Institute) who led the research said: "this research will streamline efforts to improve barley production through breeding for improved varieties. This could be varieties better able to withstand pests and disease, deal with adverse environmental conditions, or even provide grain better suited for beer and brewing".

Nature. 2012 Oct 17. doi: 10.1038/nature11543.

A physical, genetic and functional sequence assembly of the barley genome.

The International Barley Genome Sequencing Consortium

Abstract

Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.

PMID:

 

23075845

Flash Report: The search for extra-terrestrial genomes

Although we are non even close to April Fools' Day, I found quite unbelievable that Craig Venter and Jonathan Rothberg, founder of Ion Torrent, are independently developing a DNA sequencing machine to be delivered to Mars to search for life.
You can have additional details about this almost unbelievable project from this Technology Review article.
By the way, I didn't know of the existence of a NASA-funded project at Harvard and MIT called SET-G, or "the search for extra-terrestrial genomes.

Flash Report: Ion great discounts!

Competition between the two NGS giants (Illumina and Life Technologies) is resulting in more and more advantages for the final users, particularly in terms of technological advancements and price rebates. 

Now that its new Proton is on the market and ready to ship, Life Technologies seems to have adopted an aggressive marketing policy offering great discounts on both PGM and Proton...

They also offer an interesting trade-in solution: 40% discount on Proton in exchange of your old Illumina GAIIx!

See the offer on the Life Technologies site!

NGS PubMed Highlights: Can we predict the face of an individual from its DNA?

Apparently we are not there yet, however a recent article published in PLoS Genetics describes a genome-wide association study that allowed the identification of five loci influencing facial morphology in europeans. The study has been carried out in almost 5,400 individuals of European descent. Researchers defined four-dozen facial traits measurable from three-dimensional magnetic resonance as well from two-dimensional data from portrait photographs.
PRDM16, PAX3, TP63, C5orf50, and COL17A1 are the five candidate genes involved in the determination of the human face.
The scientists involved in the study speculate that it should be possible to identify additional variants, including some with smaller effects, through studies that involve larger sample sets and more detailed facial measurements.
As reported by the Medical Daily web site "perhaps one day, police officers will be able to use DNA found at the crime scene to create an image of a person's face, rather than relying on witness testimony told to sketch artists".

PLoS Genet. 2012 Sep;8(9):e1002932. doi: 10.1371/journal.pgen.1002932. Epub 2012 Sep 13.

A genome-wide association study identifies five Loci influencing facial morphology in europeans.

Liu F, van der Lijn F, Schurmann C, Zhu G, Chakravarty MM, Hysi PG, Wollstein A, Lao O, de Bruijne M, Ikram MA, van der Lugt A, Rivadeneira F, Uitterlinden AG, Hofman A, Niessen WJ, Homuth G, de Zubicaray G, McMahon KL, Thompson PM, Daboul A, Puls R, Hegenscheid K, Bevan L, Pausova Z, Medland SE,Montgomery GW, Wright MJ, Wicking C, Boehringer S, Spector TD, Paus T, Martin NG, Biffar R, Kayser M.

Source

Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.

Abstract

Inter-individual variation in facial shape is one of the most noticeable phenotypes in humans, and it is clearly under genetic regulation; however, almost nothing is known about the genetic basis of normal human facial morphology. We therefore conducted a genome-wide association study forfacial shape phenotypes in multiple discovery and replication cohorts, considering almost ten thousand individuals of European descent from several countries. Phenotyping of facial shape features was based on landmark data obtained from three-dimensional head magnetic resonance images (MRIs) and two-dimensional portrait images. We identified five independent genetic loci associated with different facial phenotypes, suggesting the involvement of five candidate genes-PRDM16, PAX3, TP63, C5orf50, and COL17A1-in the determination of the human face. Three of them have been implicated previously in vertebrate craniofacial development and disease, and the remaining two genes potentially represent novel players in the molecular networks governing facial development. Our finding at PAX3 influencing the position of the nasion replicates a recent GWAS of facialfeatures. In addition to the reported GWA findings, we established links between common DNA variants previously associated with NSCL/P at 2p21, 8q24, 13q31, and 17q22 and normal facial-shape variations based on a candidate gene approach. Overall our study implies that DNA variants in genes essential for craniofacial development contribute with relatively small effect size to the spectrum of normal variation in human facialmorphology. This observation has important consequences for future studies aiming to identify more genes involved in the human facial morphology, as well as for potential applications of DNA prediction of facial shape such as in future forensic applications.

PMID:

 

23028347

PubMed Highlight: Challenges and Opportunities of Next-Generation Sequencing for Biomedical Research

Advances in Protein Chemistry and Structural Biology has dedicated an entire volume to NGS technology:

1. Chapter One - Next Generation Sequencing Methodologies - An Overview
2. Chapter Two - Next Generation Sequencing in the Clinical Domain: Clinical Advantages, Practical, and Ethical Challenges
3. Chapter Three - Opportunities and Challenges for Genome Sequencing in the Clinic
4. Chapter Four - Polymorphisms in Neuropsychiatric and Neuroinflammatory Disorders and the Role of Next Generation Sequencing in Early Diagnosis and Treatment
5. Chapter Five - Structural Modelling Pipelines in Next Generation Sequencing Projects

That's sure worth a look!

Vela Diagnostic announce develop of diagnostic test on Ion Torrent PGM

Vela Diagnostics has just announced that it has start developing new molecular diagnostic test on the Ion Torrent PGM. Thank to a partnership with Life Technologies, they will have access to the full spectrum of available chips and reagents to develop and optimize their new tests (see the full press-release).

The new kits, announced for 2014, will aim oncology and infectious diseases, where the company has a well established expertise, selling tests for influenza, norovirus, and hepatitis C and B viruses. However CEO Michael Tillmann has declared that the access to NGS technology allow the team to grow according to market demands and eventually move to whole-exome or whole-genome tests.

VelaDx plans to seek regulatory approval for its tests, including clearance from the US Food and Drug Administration and also Life Tech has said that it plans to seek FDA 510(k) clearance for the PGM.

Flash Report: The Nobel Prize in Physiology or Medicine 2012 to Yamanaka and Gurdon

From the official Press Release published on the web site of the Nobel Prize:

"The Nobel Prize recognizes two scientists who discovered that mature, specialised cells can be reprogrammed to become immature cells capable of developing into all tissues of the body. Their findings have revolutionised our understanding of how cells and organisms develop.

John B. Gurdon discovered in 1962 that the specialisation of cells is reversible. In a classic experiment, he replaced the immature cell nucleus in an egg cell of a frog with the nucleus from a mature intestinal cell. This modified egg cell developed into a normal tadpole. The DNA of the mature cell still had all the information needed to develop all cells in the frog.

Shinya Yamanaka discovered more than 40 years later, in 2006, how intact mature cells in mice could be reprogrammed to become immature stem cells. Surprisingly, by introducing only a few genes, he could reprogram mature cells to become pluripotent stem cells, i.e. immature cells that are able to develop into all types of cells in the body.

These groundbreaking discoveries have completely changed our view of the development and cellular specialisation. We now understand that the mature cell does not have to be confined forever to its specialised state. Textbooks have been rewritten and new research fields have been established. By reprogramming human cells, scientists have created new opportunities to study diseases and develop methods for diagnosis and therapy."

NGS PubMed Highlights: Researchers sequence and analyze whole genomes of seven infants in about 50 hours!

A team led by Stephen Kingsmore used an Illumina HiSeq 2500 to sequence the genomes of seven babies that died near birth. The 50 hour screening time was not due to sequencing speed, but rather analysis speed.
As discussed in an editorial published on SingularityHUB  "... it took about four and a half hours to prepare the samples and another twenty-five and half hours to sequence the genomes with the HiSeq machine. The remaining 20 hours then was all it took to analyze the entire 3.2 billion base pairs of the genomes and pinpoint causal mutations. They were able to achieve such efficiency by modifying their analysis software to be both automated and smart. Much of what is normally performed manually, like finding a mutation and associating it with a disease, was carried out by software. In addition, the clinical features of the babies were taken into account such that the software focused on genes that were most likely linked to the symptoms, greatly decreasing the analysis workload. And quality was not sacrificed for speed. Retrospectively diagnosing the critical illnesses of five out of seven babies demonstrates that the system could make a huge difference in a clinical setting".

The study was published recently in Science Translational Medicine.

Sci Transl Med. 2012 Oct 3;4(154):154ra135. doi: 10.1126/scitranslmed.3004041.

Rapid whole genome sequencing for genetic disease diagnosis in neonatal intensive care units.

Saunders CJ, Miller NA, Soden SE, Dinwiddie DL, Noll A, Alnadi NA, Andraws N, Patterson ML, Krivohlavek LA, Fellis J, Humphray S, Saffrey P, Kingsbury Z,Weir JC, Betley J, Grocock RJ, Margulies EH, Farrow EG, Artman M, Safina NP, Petrikin JE, Hall KP, Kingsmore SF.

Source

Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA.

Abstract

Monogenic diseases are frequent causes of neonatal morbidity and mortality, and disease presentations are often undifferentiated at birth. More than 3500 monogenic diseases have been characterized, but clinical testing is available for only some of them and many feature clinical and geneticheterogeneity. Hence, an immense unmet need exists for improved molecular diagnosis in infants. Because disease progression is extremely rapid, albeit heterogeneous, in newborns, molecular diagnoses must occur quickly to be relevant for clinical decision-making. We describe 50-hour differential diagnosis of genetic disorders by whole-genome sequencing (WGS) that features automated bioinformatic analysis and is intended to be a prototype for use in neonatal intensive care units. Retrospective 50-hour WGS identified known molecular diagnoses in two children. Prospective WGS disclosed potential molecular diagnosis of a severe GJB2-related skin disease in one neonate; BRAT1-related lethal neonatal rigidity and multifocal seizure syndrome in another infant; identified BCL9L as a novel, recessive visceral heterotaxy gene (HTX6) in a pedigree; and ruled out known candidate genes in one infant. Sequencing of parents or affected siblings expedited the identification of disease genes in prospective cases. Thus, rapid WGS can potentially broaden and foreshorten differential diagnosis, resulting in fewer empirical treatments and faster progression togenetic and prognostic counseling.

PMID:

 

23035047