Publications

The following compilation is a list of published references using Rubicon technology.

2011
Bosso Mira, Al-Mulla Fahd. Formalin-Fixed Paraffin-Embedded Tissues: Methods and Protocols. Methods in Molecular Biology. 2011 724: 161-180
A good review of use of GenomePlex WGA for genetic analysis of FFPE tissue.

Png Eileen, Thalamuthu Anbupalam, Ong Rick TH, Snippe Harm, Boland Greet J, Seielstad Mark. A Genome Wide Association Study of Hepatitis B Vaccine Response in an Indonesian Population Reveals Multiple Independent Risk Variants in the HLA Region. Human Molecular Genetics, Advance Access, 2011, July 15
Rubicon DNA extraction and whole genome amplification was used to prepare frozen serum samples for genotyping 4576 individuals who had participated in an HBV vaccine trial.

Kim Jung H, Dhanasekaran Saravana M., Prensner John R., Cao Xuhong,
Robinson Daniel, Kalyana-Sundaram Shanker, Huang Christina, Shankar Sunita, Jingo Xiaojun, Iyer Matthew, Hu Ming, Sam Lee, Grasso Catherine,. Maher Christopher A, Palanisamy Nallasivam, Mehra Rohit, Kominsky Hal D, Siddiqui Javed, Yu Jindan, Qin Zhaohui S,. Chinnaiyan Arul M. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome Research. 2011 21: 1028-1041
This is a milestone paper using the Rubicon MethylPlex NGS prep for methylation profiling by next-generation sequencing.

Fiorentino F, Spizzichino L, Bono S, Biricik A, Kokkali G, Rienzi L, Ubaldi FM, Lammarrone E, Gordon A, Pantos K. PGD for reciprocal and Robertsonian translocations using array comparative genomic hybridization. Human Reproduction, 2011 Vol.26 (7), 1925–1935
The Rubicon PicoPlex™ WGA (distributed under the trademark SurePlex™ by BlueGnome) was used to amplify single human blastomeres for microarray detection of chromosome translocations before implantation. The results show improved accuracy of aneuploidy and reciprocal translocation detection compared to FISH-based testing.

Hornak Miroslav, Jeseta Michal, Musilova Petra, Pavlok Antonin, Kubelka Michal, Motlik Jan, Rubes Jiri, Anger Martin. Frequency of Aneuploidy Related to Age in Porcine Oocytes. PLoS ONE 2011, April, 6(4), 1-5
In the porcine model organism, PicoPlex™ WGA was shown to improve detection of aneuploidy of oocytes compared to FISH testing.

Navin Nicholas, Hicks James. Future Medical Applications of Single-Cell Sequencing in Cancer. Genome Medicine, 2011 3(31)
Very good review of the methods and medical applications of single cell sequencing, including using GenomePlex WGA for next-gen sequencing of single cells.

Navin Nicholas, Kendall Jude, Troge Jennifer, Andrews Peter, Rodgers Linda, McIndoo Jeanne, Cook Kerry, Stepansky Asya, Levy Dan, Esposito Diane, Muthuswamy Lakshmi, Krasnitz Alex, McCombie W. Richard, Hicks James, Wigler Michael. Tumour Evolution Inferred by Single-Cell Sequencing. Nature 2011, 472, 90-94
GenomePlex WGA amplification of single human nuclei was used to accurately determine copy number variations in tumor cell populations. This was used to reconstruct evolution of a heterogeneous population of cancer cells.

Gutierrez-Mateo Cristina, Colls Pere, Sanchez-Garcia Jorge, Escudero Tomas, Prates Renata, Ketterson Kelly, Wells Dagan, Munne Santiago. Validation of micro array comparative genomic hybridization for comprehensive chromosome analysis of embryos. Fertility and Sterility, March 1, 2011, Vol. 95(3), 953-958
This landmark study concluded that PicoPlex WGA (distributed as SurePlex by BlueGnome) had almost 4 times fewer analysis failures and almost 5 times fewer misdiagnoses than GenomePlex WGA (distributed by Sigma-Aldrich).

Alfarawati S., Fragouli E, Colls P., Wells D.. First births after pre-implantation genetic diagnosis of structural chromosome abnormalities using comparative genomic hybridization and micro array analysis. Human Reproduction, 2011 Vol.26 (6), 1560–1574
This landmark study documents the first births after PGD of chromosomal abnormalities using single cell aCGH, which used the Rubicon PicoPlex WGA process (distributed as SurePlex by BlueGnome).

Yang Hong, Chen Xi, Hung Wong Wing. Completely Phased Genome Sequencing through Chromosome Sorting. PNAS January 4, 2011, vol. 108, 12–17
PicoPlex WGA was used with a home-brew method of adding NGS adaptor sequences to sequence single-copy sorted chromosomes to infer the haplotype of individual human chromosomes.

2010
Navin Nicholas, Hicks James. Tracing the Tumor Lineage. Molecular Oncology 2010, vol. 4, 267-283
Wang Jianhua, Ying Gigi, Wang Jingchen, Jung Younghun, Lu Jian, Zhu Jiang, Pienta Kenneth J., Taichman Russell S. Characterization of PGK1 Expression by Stromal Cells Derived from the Tumor Microenvironment in Prostate Cancer Progression. Cancer Research, 2010 January 15; 70(2): 471-480
TransPlex WTA was used for microarray expression studies of 5,000 – 10,000 microdissected prostate cancer cells.

Luan, S.-L., Boulanger, E., Ye, H., Chanudet, E., Johnson, N., Hamoudi, R. A., Bacon, C. M., Liu, H., Huang, Y., Said, J., Chu, P., Clemen, C. S., Cesarman, E., Chadburn, A., Isaacson, P. G. and Du, M.-Q. (2010), Primary effusion lymphoma: genomic profiling revealed amplification of SELPLG and CORO1C encoding for proteins important for cell migration. The Journal of Pathology, 2010 July; 222(2): 166–179
GenomePlex WGA was used to amplify small numbers of cancer cells for array CGH

Luo W, Wu F, Atlas SR, Pickett G, Leslie KK, Dai D. Defining Genetic Intra-tumor Heterogeneity: A Chronological Annotation of Mutational Pathways. Proceedings in Obstetrics and Gynecology, 2010 Apr; 1(1): Article 9, [14 pp]
GenomePlex WGA is used to amplify small numbers of tumor cells for genotyping to understand tumor progression.

Hong Yang, Xi Chen, and Wing Hung Wong. Completely phased genome sequencing through chromosome sorting. Inaugural article. PNAS 2011 108 (1) 12-17; published ahead of print December 15, 2010, doi:10.1073/pnas.1016725108. Available online.

Beck, B. Urnovitz, HB. Mitchell, WM. Schutz, E. Next Generation Sequencing of Serum Circulating Nucleic Acids from Patients with Invasive Ductile Breast Cancer Reveals Differences to Healthy and Nonmalignant Controls. Mol Cancer Res 8(3):335-342, 2010.
Use of GenomePlex WGA to amplify circulating DNA for sequencing on the 454/Roche GS-FLX platform.

Beck, J. Urnovitz, HB. Saresella, M. Mitchell, WM. and Schutz, E. Serum DNA Motifs Predict Disease and Clinical Status in Multiple Sclerosis. J Mol Diagn 2010.
Use of GenomePlex WGA to detect multiple sclerosis from serum.

Davila, S. Froeling FEM. Tan, A. Bonnard, C. Snippe, H. Hibberd, ML. New genetic associations detected in a host response study to hepatitis B vaccine. Genes and Immunity (2010) 1-7

Gonzalez-Roca, E. Garcia-Albeniz, X. Rodriguez-Mulero, S. Gomis, RR. Kornacker, K. Auer, H. Accurate Expression Profiling of Very Small Cell Populations. PLoS ONE 5(12):e14418, 2010.
Accurate expression profiling from as few as 10 cells using the Sigma TransPlex WGA2 kits

Gutiérrez-Mateo, C. Colls, P. Sánchez-Garcia, J. Escudero, T. Prates, R. Ketterson, K. Wells, D. Munné, S. Validation of microarray comparative genomic hybridization for comprehensive chromosome analysis of embryos. Original research artilcle. Fertility and Sterility, available online, 2010.

Northrop, LE. Treff, NR. Levy, B. Scott Jr., RT. SNP microarray-based 24 chromosome aneuploidy screening demonstrates that cleavage-stage FISH poorly predicts aneuploidy in embryos that develop to morphologically normal blastocysts. Molecular Human Biology 16(8)m art, no. gaq037:590-600, 2010.

Schutz, E. Beck, J. Mitchell, WM. Urnovitz. Comparative analysis of the chromosomal origins of circulating nucleic acids in breast and prostate cancer. J Clin Oncol 28:7s 2010 (suppl: abstr 10505).
Use of GenomePlex WGA of serum to detect breast and prostate cancer using massively-parallel sequencing.

Sell, E. Robert, C. Sirard, MA. Omics in assisted reproduction: Possibilities and pitfalls. Molecular Human Reproduction 16(8), art. no. gaq041:513-530, 2010.

Treff, NR. Levy, B. Su, J. Northrop, LE. Tao, X. Scott Jr., RT. SNP microarray-based 24 chromosome aneuploidy screening is significantly more consistent than FISH. Molecular Human Biology 16(8), art. no. gaq039:583-589, 2010.

2009
Chung, Y. Bishop CE. Treff, NR. Walker, SJ. Sandlre, VM. Becker, S. Klimanskaya, I. Wun, WS. Dunn, R. Hall, RM. Su J. Lu, SJ. Maserati, M. Choi, YH. Scott, R., Atala, A. Dittman R. Lanza, R. Reprogramming of Human Somatic Cells Using Human and Animal Oocytes. Cloning and Stem Cells 11(2) 2009.
GenomePlex WGA used to karyotype, genotype, and sequence single human blastomeres.

Gordon, PMK. Schutz, E. Beck, J. Urnovitz, HB. Graham, C. Clark, R. Dudas, S. Czub, S. Sensen, M. Brenig, B. Groschup, MH. Church, RB. Sensen, CW. Disease-specific motifs can be identified in circulating nucleic acids from live elk and cattle infected with transmissible spongioform encyphalopathies. Nucl Acids Res 37(2):550-556 (2009).
Use of GenomePlex WGA of serum DNA for early detection of BSE using Roche/454 GS-FLx.

Steiner, LA. Maksimova, Y. Schulz, V. Wong, C. Raha D. Mahajan MC. Weissman, SM. Gallagher PG. Chromatin Architecture and Transcription Facotr Binding Regulate Expresion of Erythrocyte Membrane Protein Genes. Mol Cell Biology 29(20):5399-412, 2009
GenomePlex WGA used for deep sequencing of ChIP DNA

2008
Bastien, R. Lewis TB. Hawkes JE. Quackenbush JF. Robbins TC. Palazzo J. Perou CM. Bernard PS. High-throughput amplicons scanning of the TP53 gene in breast cancer using high-resolution fluorescent melting curve analyses and automatic mutation calling. Human Mutation 29(5):757-764, 2008.
GenomePlex gave superior results for mutation detection in FFPE tissue.

Chen, SU. Su, YN. Fang, MY. Chang LJ. Tsai Y-Y. Lin, LT. Lee, C-N Yang, Y-S. PGD of beta-thalassaemia and HLA haplotypes using OmniPlex whole genome amplification. Reproductive BioMedicine Online, 17(5):699-705, 2008
GenomePlex used to increase the success rates of PGD using STR and mutation assays.

Laxman et al. (2008) A First-generation Multiplex Biomarker Analysis of Urine for the Early Diagnosis of Prostate Cancer. Cancer Research, 68:645-649.
Use of TransPlex for discovery of expression biomarkers in urine.

Mead S. Poulter M. Beck J. Uphill J. Jones C. Ang CE. Mein CA. Collinge J. Successful amplification of degraded DNA for use with high-throughput SNP genotyping platforms. Human Mutation 0:1-7, 2008 (advance publication).
GenomePlex gave superior genotyping results for amplifying DNA from degraded DNA.

2007
Mizutani Tetsuya, Endoh Daiji, Okamoto Michiko, Shirato Kazuya, Shmizu Hiroyuki, Arita Minertaro, Fukushi Shuetsu, Saijo Masayuki, Sakai Kouji, Lim Chang Kweng, Ito Mikako, Nerome Reiko, Takasaki Tomohiko, Ishii Koji, Suzuki Tetsuro, Kurane Ichiro, Morikawa Shigeru, Nishimura Hidekazu. Rapid Genome Sequencing of RNA Viruses. Emerging Infectious Diseases, www.cdc.gov/eid, 2007 Feb; 13(2):322-324
GenomePlex WGA and TransPlex WTA was used to amplify cDNA to enable rapid determination of viral RNA sequences.

Ballantyne KN. van Oorschot RA. Mitchell RJ. Comparison of two whole genome amplification methods for STR genotyping of LCN and degraded DNA samples. Forensic Science International. 166(1):35-41, 2007 Feb 14.

Coskun S. Alsmadi O. Whole genome amplification from a single cell: a new era for preimplantation genetic diagnosis. Prenatal Diagnosis. 27(4):297-302, 2007 Apr

Fiegler H. Geigl JB. Langer S. Rigler D. Porter K. Unger K. Carter NP. Speicher MR. High resolution array-CGH analysis of single cells. Nucleic Acids Research. 35(3):e15, 2007.
Shows that GenomePlex can be used for single-cell CGH.

Geigl JB. Speicher MR. Single-cell isolation from cell suspensions and whole genome amplification from single cells to provide templates for CGH analysis. Nature Protocols. 2(12):3173-84, 2007.
Single-cell array CGH using GenomePlex WGA.

Hittelman A. Sridharan S. Roy R. Fridly and J. Loda M. Collins C. Paris PL. Evaluation of whole genome amplification protocols for array and oligonucleotide CGH. Diagnostic Molecular Pathology. 16(4):198-206, 2007 Dec.

Iwamoto K. Ueda J. Nakano Y. Bundo M. Ukai W. Hashimoto E. Saito T. Kato T. Evaluation of whole genome amplification methods using postmortem brain samples. Journal of Neuroscience Methods. 165(1):104-10, 2007 Sep 15.

Kim et al. (2007) Integrative Analysis of Genomic Aberrations Associated with Prostate Cancer Progression. Cancer Research 67:8229-8239.

Leanza SM. Burk RD. Rohan TE. Whole genome amplification of DNA extracted from hair samples: potential for use in molecular epidemiologic studies. Cancer Detection & Prevention. 31(6):480-8, 2007.
Shows that GenomePlex WGA of hair can be used for SNP genotyping

Peng W. Takabayashi H. Ikawa K. Whole genome amplification from single cells in preimplantation genetic diagnosis and prenatal diagnosis. European Journal of Obstetrics, Gynecology, & Reproductive Biology. 131(1):13-20, 2007 Mar.

Protopopov, A. Analysis of Genomic Copy Number Alterations Using Agilent Oligo 244K Microarray and WGA. The Cancer Genome Atlas Newsletter. September 2007.
GenomePlex WGA gives excellent oligonucleotide array CGH results.

Sorensen KM. Jespersgaard C. Vuust J. Hougaard D. Norgaard-Pedersen B. Andersen PS. Whole genome amplification on DNA from filter paper blood spot samples: an evaluation of selected systems. Genetic Testing. 11(1):65-71, 2007.
GenomePlex was validated for genotyping of DNA extracted from Guthrie cards.

Tomlins et al. (2007) Integrative Molecular Concept Modeling of Prostate Cancer Progression. Nature Genetics, 39:41-51
Uda A. Tanabayashi K. Fujita O. Hotta A. Yamamoto Y. Yamada A. Comparison of whole genome amplification methods for detecting pathogenic bacterial genomic DNA using microarray. Japanese Journal of Infectious Diseases. 60(6):355-61, 2007.
GenomePlex validated for unbiased amplification of bacterial DNA for microarray analysis.

2006
Johnson Nicola A, Hamoudi Rifat A, Ichimura Koichi, Liu Lu, Pearson Danit M, Collins V Peter, Du Ming-Qing. Application of Array CGH on Archival Formalin-Fixed Paraffin-Embedded Tissues including Small Numbers of Microdissected Cells. Laboratory Investigation, 2006 June; 86, 968-978
GenomePlex WGA was used for successful array CGH of as few as 2,000 tumor cells microdissected from FFPE tissue, and from 10 - 20 ng of DNA from FFPE samples.

Paik Soonmyung. Methods for Gene Expression Profiling in Clinical Trials of Adjuvant Breast Cancer Therapy. Clinical Cancer Research, 2006 February, 12(3), 1019-1023

Barnes KC. Grant A. Gao P. Baltadjieva D. Berg T. Chi P. Zhang S. MA, Zambelli-Weiner A. Ehrlich E. Zardkoohi O. Brummet ME. Stockton M. Watkins T. Gao L. Gittens M. Wills-Karp M. Cheadle C. Beck LA. Beaty TH. Becker KG. Garcia JGN. Mathias RA. Polymorphisms in the novel gene acyloxyacylhydroxylase (AOAH) are associated with asthma and associated phenotypes. J. Allergy and Clinical Immunology. 118:70 – 77, 2006.
GenomePlex WGA for large SNP study on Illumina platform.

Laxman et al. (2006) Noninvasive Detection of TMPRSS2:ERG Fusion Transcripts in the Urine of Men with Prostate Cancer. Neoplasia, 8:885-888.

Little SE. Vuononvirta R. Reis-Filho JS. Natrajan R. Iravani M. Fenwick K. Mackay A. Ashworth A. Pritchard-Jones K. Jones C. Array CGH using whole genome amplification of fresh-frozen and formalin-fixed, paraffin-embedded tumor DNA. Genomics. 87(2):298-306, 2006 Feb.
Superior results with GenomePlex WGA for FFPE material.

O’Geen H. Nicolet CM. Blahnik K. Green R. Farnham PJ. Comparison of sample preparation methods for ChIP-chip assays. Biotechniques. 41(5):577-80, 2006 Nov.
Adopted GenomePlex as superior to ligation-mediated PCR because of higher S/N ratio.

Peano C. Severgnini M. Cifola I. De Bellis G. Battaglia C. Transcriptome amplification methods in gene expression profiling. Expert Review of Molecular Diagnostics. 6(3):465-80, 2006 May.

Tomlins et al. (2006). Whole Transcriptome Amplification for Gene expression Profiling and Development of Molecular Archives. Neoplasia, 8: 153-162.

2005
Bergen AW. Haque KA. Qi Y. Beerman MB. Garcia-Closas M. Rothman N. Chanock SJ. Comparison of yield and genotyping performance of multiple displacement amplification and OmniPlex whole genome amplified DNA generated from multiple DNA sources. Human Mutation. 26(3):262-70, 2005.
GenomePlex amplimers are too small to genotype using a specific set of forensic STRs. (In research studies GenomePlex DNA produced excellent genotyping using the complete well-known Marshfield STR panel).

2004
Barker DL. Hansen MS. Faruqi AF. Giannola D. Irsula OR. Lasken RS. Latterich M. Makarov V. Oliphant A. Pinter JH. Shen R. Sleptsova I. Ziehler W. Lai E. Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel. Genome Research. 14(5):901-7, 2004 May.
GSK and Illumina study shows 99.8% SNP genotype concordance between GenomePlex amplified DNA and unamplified human genomic DNA.

Gribble SM. Fiegler H. Burford DC. Prigmore E. Yang F. Carr P. Ng BL. Sun T. Kamberov ES. Makarov VL. Langmore JP. Carter NP. Applications of combined DNA Microarray and Chromosome Sorting Technologies. Chromosome Research 12:35-43, 2004.
GenomePlex WGA from single-copy sorted chromosomes gives excellent array CGH.

Gribble S. Ng BL. Prigmore E. Burford DC. Carter NP. Chromosome paints from single copies of chromosomes. Chromosome Research. 12(2):143-51, 2004.
GenomePlex WGA of individual sorted chromosomes can synthesize excellent FISH probes for CGH.

Hughes S. Lim G. Beheshti B. Bayani J. Marrano P. Huang A. Squire JA. Use of whole genome amplification and comparative genomic hybridisation to detect chromosomal copy number alterations in cell line material and tumour tissue. Cytogenetic & Genome Research. 105(1):18-24, 2004.