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Search Publications by: Peter M. Vallone (Fed)

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Displaying 26 - 50 of 98

One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation

May 18, 2021
Author(s)
Stephen Lincoln, Tina Hambuch, Justin Zook, Sara Bristow, Kathryn Hatchell, Rebecca Truty, Michael Kennemer, Brian Shirts, Andrew Fellowes, Shimul Chowdhury, Eric Klee, Shazia Mahamdallie, Megan Cleveland, Peter Vallone, Yan Ding, Sheila Seal, Wasanthi DeSilva, Farol Tomson, Catherine Huang Huang, Russell Garlick, Nazneen Rahman, Marc L. Salit, Stephen Kingsmore, Matthew Ferber, Swaroop Aradhya, Robert Nussbaum
Next-generation sequencing (NGS) is widely used and cost-effective. However, depending on the specific methods used, NGS can have limitations with certain technically challenging variant types. These types are poorly represented in some validation studies

Cautionary Note on Contamination of Reagents Used for Molecular Detection of SARS-CoV-2

May 3, 2021
Author(s)
Peter Vallone, James Huggett, Vladimir Benes, Jeremy Garson, Kathryn Harris, Mikael Kubista, Timothy McHugh, Jacob Moran-Gilad, Tania Nolan, Michael Pfaffl, Marc Salit, Greg Shipley, Jo Vandesompele
Reverse transcription (RT)-PCR, the principal diagnostic method applied in the world-wide struggle against COVID-19, is capable of detecting a single molecule of a viral genome. Correctly designed and practiced RT-PCR assays for SARS-CoV-2 should not cross

Revision of the SNPforID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies

May 3, 2021
Author(s)
John Butler, Manuel Fondevila, Carla Santos, Ana Freire, Christopher Phillips, M Lareu, Peter Vallone
A revision of an established 34 SNP forensic ancestry test has been made by swapping the under- performing rs727811 component SNP with the highly informative rs3827760 that shows a near-fixed East Asian specific allele. We collated SNP variability data for

Sequence-based U.S. population data for 7 X STR loci

April 26, 2021
Author(s)
Lisa Borsuk, Carolyn R. Steffen, Kevin M. Kiesler, Peter Vallone, Katherine Gettings
The National Institute of Standards and Technology (NIST) U.S. population sample set of unrelated individuals was used to determine allele and haplotype frequencies for seven X-chromosome short tandem repeat (STR) loci in four linkage groups. DXS7132

NIST Scientific Foundation Reviews

December 18, 2020
Author(s)
John M. Butler, Hariharan K. Iyer, Richard A. Press, Melissa Taylor, Peter Vallone, Sheila Willis
The National Institute of Standards and Technology (NIST) is a scientific research agency that works to advance measurement science, standards, and technology and that has been working to strengthen forensic science methods for almost a century. In recent

Classification of STR allelic variation using massively parallel sequencing and assessment of flanking region power

July 12, 2020
Author(s)
Laurence Devesse, Lucinda Davenport, Lisa Borsuk, Katherine Gettings, Gabriella Mason-Buck, Peter Vallone, David Ballard
The application of massively parallel sequencing (MPS) to forensic genetics has led to improvements in multiple aspects of DNA analysis, however, additional complexities are concurrently associated with these advances. In relation to short tandem repeat

DNA mixture interpretation principles: insights from the NIST scientific foundation review

July 1, 2020
Author(s)
John Butler, Hariharan K. Iyer, Richard A. Press, Melissa Taylor, Peter Vallone, Sheila Willis
DNA mixture interpretation has become more challenging in recent years due to several factors including submission of more touch evidence samples to aid investigations and generation of more sensitive DNA test results with new STR typing kits. This

Results of the 2018 Rapid DNA Maturity Assessment

January 27, 2020
Author(s)
Erica L. Romsos, Peter Vallone
Three commercially available integrated rapid DNA instruments were tested as a part of a rapid DNA maturity assessment in the July of 2018. The assessment was conducted with sets of blinded single-source reference samples to gauge the typing success of the

Understanding the characteristics of sequence-based single-source DNA profiles

November 9, 2019
Author(s)
Sarah Riman, Hariharan K. Iyer, Lisa A. Borsuk, Peter M. Vallone
The sequencing of STR markers provides additional information present in the underlying sequence variation that is typically masked by traditional fragment-based genotyping. However, the interpretation of STR profiles generated by targeted sequencing

Are Reported Likelihood Ratios Well Calibrated?

October 8, 2019
Author(s)
Peter Vallone, Sarah Riman, Jan Hannig
In this work we introduce a new statistical methodology for empirically examining the validity of model-based Likelihood Ratio (LR) systems by applying a general statistical inference approach called generalized fiducial inference [1]. LR systems are

2018 Rapid DNA Maturity Assessment Results

September 26, 2018
Author(s)
Erica L. Romsos, Peter Vallone
The Rapid DNA Act, which amends the DNA Identification Act of 1994, allows for the integration of rapid DNA instruments for use by law enforcement for DNA testing of arrestees in a booking station environment. Several parallel efforts have been made to

Certification of Standard Reference Material 2365 BK Virus DNA Quantitative Standard

August 29, 2018
Author(s)
Megan H. Cleveland, Natalia Farkas, Kevin M. Kiesler, Blaza Toman, Peter M. Vallone
Standard Reference Material (SRM) 2365 is intended for use in the value assignment of BK virus deoxyribonucleic acid (DNA) to BK DNA controls and standards. A unit of SRM 2365 consists of a well characterized, linearized plasmid, containing BK virus DNA

Sequence-based U.S. population data for 27 autosomal STR loci

July 19, 2018
Author(s)
Katherine Gettings, Lisa Borsuk, Carolyn R. Steffen, Kevin M. Kiesler, Peter Vallone
This manuscript reports STR sequence-based allele frequencies for the "NIST 1036" sample set across 27 autosomal STR loci: D1S1656, TPOX, D2S441, D2S1338, D3S1358, D4S2408, FGA, D5S818, CSF1PO, D6S1043, D7S820, D8S1179, D9S1122, D10S1248, TH01, vWA

Sequence-based U.S. population data for the SE33 locus

May 7, 2018
Author(s)
Lisa Borsuk, Katherine Gettings, Carolyn R. Steffen, Kevin M. Kiesler, Peter Vallone
A set of 1036 U.S. Population Samples were sequenced using the Illumina ForenSeq DNA Signature Prep Kit. This sample set has been highly characterized using a variety of marker systems for human identification. The FASTQ files obtained from a ForenSeq DNA

STRSeq: A catalog of sequence diversity at human identification Short Tandem Repeat loci

November 1, 2017
Author(s)
Katherine Gettings, Lisa Borsuk, D Ballard, Martin Bodner, Bruce Budowle, Laurence Devesse, Jonathan King, W. Parson, Christopher Phillips, Peter Vallone
The STR Sequencing Project (STRSeq) was initiated to facilitate the description of sequence- based alleles at the Short Tandem Repeat (STR) loci targeted in human identification assays. This international collaborative effort, which has been endorsed by

Sequence variation of 22 autosomal STR loci detected by next generation sequencing

December 1, 2015
Author(s)
Katherine Gettings, Kevin M. Kiesler, Seth A. Faith, Elizabeth Montano, Christine H. Baker, Brian A. Young, Richard A. Guerreri, Peter Vallone
Sequencing short tandem repeat (STR) loci allows for determination of repeat motif variations within the STR (or entire PCR amplicon) which cannot be ascertained by size-based PCR fragment analysis. Sanger sequencing has been used in research laboratories

Sequence-based Analysis of Stutter at STR Loci: Characterization and Utility

September 23, 2015
Author(s)
Rachel A. Aponte, Katherine Gettings, David L. Duewer, Michael D. Coble, Peter Vallone
The development of next generation sequencing (NGS) technologies creates the potential for changing the method by which the forensic science community genotypes short tandem repeat (STR) loci. While the capabilities of NGS are promising, moving from