Los Alamos using cutting-edge sequencing, finishing, and analysis, impact valuable genomic data.
State-of-the art technology and extensive genomics expertise
With a rich history in genomic science, and an outstanding program in cutting-edge sequencing, finishing, and analysis, Los Alamos is poised to impact many areas of research through applying valuable genomic data. The Genome Science Program offers:
- Next generation sequencing (NGS) services on a contract basis
- Collaboration to solve complex biological problems
- In-house research projects that heavily rely on genomic and transcriptomic data
Current and past projects and scientific interests:
- Bacterial and viral genome sequencing in pure cultures and metagenomic samples (environmental and clinical)
- Infectious disease (diagnostics, outbreaks, genotype to phenotype) and global biosurveillance
- Pathogenesis (host-pathogen interactions)
- Single cell genomics and transcriptomics
- Community (microbiome) profiling and metabolism (soils, water, intestine, etc.)
- Community interactions (e.g. algal ponds, intestine, etc.)
- Transcriptomics (gene expression and structure, splice variants, small RNAs)
- Biofuel production (pond health, strain improvement, etc.)
- Cancer (drug resistance)
- Functional genomics (novel or improved enzymes, novel regulatory mechanisms, systems biology)
- Toxicology (biomarker ID, exposure quantification, mechanisms)
- Conservation of endangered and revival of extinct species
- Therapeutics (vaccine design, antibodies)
- Synthetic biology (de novo and trans-genomics)
- Human microbiome and disease
- Personalized medicine • Microbial forensics
- Human forensics and biometrics
Los Alamos’ modern sequencing, molecular biology, microbiology, and cell culture equipment are housed in a large space comprising multiple BSL-1 and BSL-2 labs. Los Alamos Lab scientists also collaborate with institutions that have BSL-3 and BSL-4 facilities.
The genome team follows strict guidelines to ensure the quality of their work, including:
- Good Laboratory Practices (GLP) whenever it is possible and practical. Most experimental processes are physically separated to prevent sample cross-contamination and ensure unchanged sample identity.
- A Laboratory Information Management System (LIMS) is used to track all samples, experimental procedures, Quality Control (QC) data, and interface the sequencers with the computer cluster.
- Regular staff training, Standard Operating Procedures and Bench Sheets are all used to ensure quality of lab tasks and data recording.
- Internal and external positive controls are used for most procedures, and an extensive Quality Assurance and Quality Control system is in place.
We currently operate five different NGS platforms:
This is a relatively low throughput, but rapid and inexpensive instrument suitable for sequencing bacterial and viral genomes and amplicons up to 400 base pairs (bp).
Our routine workflow uses 316 chips that generate >3 million reads. Combined with 400 bp sequencing kits, the total data output is generally >600 Mbps.
This is the newest instrument at Los Alamos Lab that promises rapid and high content sequencing. With the current chips (PI v2, ~80 million reads) and 200 bp sequencing kits, each run produces ~10 Gbp of sequencing data, enabling sequencing of prokaryotic genomes or transcriptomes, or eukaryotic transcriptomes.
- DNA & RNA preparation from environmental samples: Cheryl Kuske & John Dunbar
- PCR primer set design from complex datasets: Jason Gans
- Genomics and metatranscriptome analysis/computation: Jean Challacombe
- Meta ‘omics approaches for complex soil communities: Cheryl Kuske
- Databases and classifiers for classification of target genes: Gary Xie
The Illumina platforms generate the bulk of sequencing data at Los Alamos. MiSeq (20-30 million reads, 150-250 bp) is used for sequencing bacterial and viral genomes, long insert paired-end libraries, amplicons, and for many R&D projects.
The HiSeq 2000 workhorse produces vast amounts of high quality sequencing data.
PacBio technology offers the longest sequencing reads, native sequencing of modified nucleotides, and is sometimes able to sequence through genomic regions that are resistant to sequencing by other technologies. PacBio data is mostly used for genome finishing, since long reads are essential for scaffolding, either via shotgun or long amplicon sequencing.
The Genome Science Program currently manages and houses 100 servers of various age and capacity, with a total of 1000 cores, 7.1 TB of RAM, and 316 TB of total usable storage. RedHat Linux, Ubuntu and Solaris 11 are used for server operating systems.
Heavy computation is handled through a grid engine cluster and a Lustre-based distributed file system.
These resources are used to support laboratory operations in performing sequence data generation, computational genome finishing, genome annotation, metagenomic assembly and analysis, and serve databases for the research community.
A host of software platforms and tools are also used including Galaxy, Ergatis, CLCbio, and Genologics LIMS.
Tracy Erkkila is the leader for the Genome Technologies team in the Genome Science Programs. Tracy looks after project management, high throughput sequencing, computational finishing, and production bioinformatics. Tracy has over 20 years of experience across a broad range of technologies. He is a certified PMP.
Shannon Johnson, PhD, PMP, is project manager interested in the application of genomic data to a variety of questions. Currently much of her efforts are involved in comparative pathogen genomics. Shannon is responsible for coordinating sample receipt and processing, through to data exchange and manuscript submission, in most of the projects undertaken.
Ashlynn Daughton is a Post-Bachelor’s student working with Armand Dichosa, Cliff Han and Krista Reitenga. She spends the bulk of her time on projects utilizing gel microdroplet technology.
Armand Dichosa, PhD, MS, is an R&D scientist involved in single cell genomics. His primary focus is to develop technologies to obtain [near] complete genomes from single cells for the purposes of improved taxonomic identification and determining metabolic relevance from the genomic perspective. His interests involve the human microbiome and various environmental communities, addressing intra-genomic species heterogeneity and cell-to-cell interactions. He also loves volleyball, running, eating, sketching, shopping, and chillin' with a good movie.
Cheryl Gleasner has a M.S. in Forensic Science, is a Research Technologist and is the Illumina NGS Technical Lead. Cheryl is interested in next generation sequencing applications for viral, bacterial, algal and metagenomic samples. She is working on implementing automation in many of the existing platforms as she is also trained on the PacBio and Ion Torrent systems.
Shunsheng Han (Cliff)
Jeena Kim has a BA in Biological Sciences (emphasis in Neurobiology, Physiology, and Behavior) and is a Post-Bachelor student working for the wet lab team. She is involved in several different processes with various samples from working with the instruments (Biomek FX & NX) to the Illumina pipeline (MiSeq & HiSeq). She also helps maintain a clean, safe, and organized laboratory atmosphere. Her interests outside the laboratory are meeting new people, being involved with church, volleyball, hiking, frisbee, traveling, experiencing new things she hasn’t done before, and TRYING to kick someone’s butt in tennis.
Kim McMurry, BA, is a research technician working primarily on the Illumina pipelines. She prepares Illumina libraries for bacterial, viral and metagenomic samples and helps maintain and operate the instruments. She is also responsible for initial QC and maintaining the inventory of incoming samples.
Beverly Parson-Quintana is an R&D technician working on Illumina and PacBio pipelines. Beverly is also heavily involved in quality control and automation. She has worked with metagenomic, bacterial and viral samples.
Xiaohong Shen (Hong), Hong is a research technologist 1, has more than 12 years of experience working in a molecular biology laboratory. She is acting a technical lead of next generation DNA Sequencing platforms such as Ion Torrent PGM, Ion Proton and previous 454. She also operates other pipelines PacBio, Illumina as well. Hong has been responsible for implementation of all programmatic pipelines with 8kb long insert Paired-End library preparation. She is participating with our DNA sequencing Research and Development Team for our single cell projects.
Momo Vuyisich, PhD, is an R&D scientist interested in using genomics in many applications. His favorite scientific topics are pathogen detection and characterization using NGS, the connection between gut flora and human health, complex microbial communities, transcriptomics, and many others. Momo is also responsible for implementation and maintenance of Good Laboratory Practices in all programmatic pipelines.
- Ahmed SA, Awosika J, Baldwin C, Bishop-Lilly KA, Biswas B, Broomall S, Chain PSG, Chertkov O, Chokoshvili O, Coyne S et al: Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2. PLoS ONE 2012, 7(11):e48228.
- Aklujkar M, Haveman S, DiDonato R, Chertkov O, Han C, Land M, Brown P, Lovley D: The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features. BMC Genomics 2012, 13(1):690.
- Anderson IJ, Tindall BJ, Rohde M, Lucas S, Han J, Lapidus A, Cheng J-F, Goodwin L, Pitluck S, Peters L et al: Complete genome sequence of Halopiger xanaduensis type strain (SH6 T ), vol. 6; 2012.
- Beckloff N, Starkenburg S, Freitas T, Chain P: Bacterial Genome Annotation. In: Microbial Systems Biology. Edited by Navid A, vol. 881: Humana Press; 2012: 471-503.
- Dichosa AEK, Fitzsimons MS, Lo C-C, Weston LL, Preteska LG, Snook JP, Zhang X, Gu W, McMurry K, Green LD et al: Artificial Polyploidy Improves Bacterial Single Cell Genome Recovery. PLoS ONE 2012, 7(5):e37387.
- Fitzsimons MS, Novotny M, Lo C-C, Dichosa AEK, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K et al: Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome Research 2013, 23(5):878-888.
- Leung K, Zahn H, Leaver T, Konwar KM, Hanson NW, Pagé AP, Lo C-C, Chain PS, Hallam SJ, Hansen CL: A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proceedings of the National Academy of Sciences 2012, 109(20):7665-7670.
- Martinez-Garcia M, Brazel DM, Swan BK, Arnosti C, Chain PSG, Reitenga KG, Xie G, Poulton NJ, Gomez ML, Masland DED et al: Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia. PLoS ONE 2012, 7(4):e35314.
- Mason OU, Hazen TC, Borglin S, Chain PSG, Dubinsky EA, Fortney JL, Han J, Holman H-YN, Hultman J, Lamendella R et al: Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J 2012, 6(9):1715-1727.
- Scholz MB, Lo C-C, Chain PSG: Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Current Opinion in Biotechnology 2012, 23(1):9-15.
- Steven B, Gallegos-Graves LV, Starkenburg SR, Chain PS, Kuske CR: Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study. Environmental Microbiology Reports 2012, 4(2):248-256.
- Venkatramanan R, Prakash O, Woyke T, Chain P, Goodwin LA, Watson D, Brooks S, Kostka JE, Green SJ: Genome Sequences for Three Denitrifying Bacterial Strains Isolated from a Uranium- and Nitrate-Contaminated Subsurface Environment. Genome Announcements 2013, 1(4).
- Vuyisich M, Sanders C, Graves S: Binding and cell intoxication studies of anthrax lethal toxin. Mol Biol Rep 2012, 39(5):5897-5903.
- Xie G, Ramirez MS, Marshall SH, Hujer KM, Lo C-C, Johnson S, Li P-E, Davenport K, Endimiani A, Bonomo RA et al: Genome Sequences of Two Klebsiella pneumoniae Isolates from Different Geographical Regions, Argentina (Strain JHCK1) and the United States (Strain VA360). Genome Announcements 2013, 1(2).
- Zhang X, Davenport KW, Gu W, Daligault HE, Munk AC, Tashima H, Reitenga K, Green LD, Han CS: Improving genome assemblies by sequencing PCR products with PacBio. Biotechniques 2012, 53(1):61-62.