John A Shepherd PhD
Researcher R5Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawai‘i Cancer Center
Work Email: johnshep@hawaii.edu
Research Interests
Dr. Shepherd has a 30-year background in quantitative imaging. Most of his academic research involves developing novel biomarkers for a variety of imaging modalities including dual-energy X-ray Absorptiometry (DXA) scan for bone density and body composition, mammography for breast density and tissue textural measures as risk factors for breast cancer, and 3-D optical whole body scanning for quantifying body shape as a risk factor for metabolic diseases. Using these modalities, he uses advanced statistical methods to extract more information from images. The methods include principal component analysis, shape and appearance modeling, deep learning, and artificial intelligence approaches. While at UCSF he accumulated over 4 million mammograms for the study of breast cancer risk from imaging and was one of the first to show that volumetric breast density measures are a stronger risk predictor than areal density measures. His active research questions include the following: • Can deep learning models for reading mammograms reduce recall rates and unnecessary biopsies for women of the Pacific region? • What is the best way to describe frailty and function using quantitative composition measures? • Can 3-D optical scans of the whole body accurately and precisely quantify body composition and other health risk factors, and improve compliance of nutrition and exercise interventions? He also holds four patents in quantitative imaging. His group has been expert consultants for the NHANES study DXA component for 20 years. He has published over 150 peer-reviewed papers, is a Fulbright Scholar, and a past president of the International Society for Clinical Densitometry.
Recent Publications
Wong, MC., Ng, BK, Kennedy, SF, Hwaung, P, Liu, EY, Kelly, NN, Pagano, IS, Garber, AK, Chow, DC, Heymsfield, SB, Shepherd, JA. (2019). Children and Adolescents’ Anthropometrics Body Composition from 3‐D Optical Surface Scans. Obesity, 27: 1738-1749. doi:10.1002/oby.22637.- Ng BK, Sommer MJ, Wong MC, Pagano I, Nie Y, Fan B, Kennedy S, Bourgeois B, Kelly N, Liu YE, Hwaung P, Garber AK, Chow D, Vaisse C, Curless B, Heymsfield SB, Shepherd JA. (2019). Detailed 3-dimensional body shape features predict body composition, blood metabolites, and functional strength: the Shape Up! studies. The American Journal of Clinical Nutrition; Dec 1;110(6):1316-1326. doi: 10.1093/ajcn/nqz218. PubMed PMID: 31553429; PubMed Central PMCID: PMC6885475.
- Drukker K, Giger ML, Joe BN, Kerlikowske K, Greenwood H, Drukteinis JS, Niell B, Fan B, Malkov S, Avila J, Kazemi L, Shepherd J. (2019). Combined Benefit of Quantitative Three-Compartment Breast Image Analysis and Mammography Radiomics in the Classification of Breast Masses in a Clinical Data Set. Radiology; Mar;290(3):621-628. doi: 10.1148/radiol.2018180608. Epub 2018 Dec 11. PubMed PMID: 30526359; PubMed Central PMCID: PMC6394732.
- Ng BK, Liu YE, Wang W, Kelly TL, Wilson KE, Schoeller DA, Heymsfield SB, Shepherd JA. (2018). Validation of rapid 4-component body composition assessment with the use of dual-energy X-ray absorptiometry and bioelectrical impedance analysis. The American Journal of Clinical Nutrition; Oct 1;108(4):708-715. doi: 10.1093/ajcn/nqy158. PubMed PMID: 30099474.
- Shepherd JA, Sommer MJ, Fan B, Powers C, Stranix-Chibanda L, Zadzilka A, Basar M, George K, Mukwasi-Kahari C, Siberry G. Advanced Analysis Techniques Improve Infant Bone and Body Composition Measures by Dual-Energy X-Ray Absorptiometry. J Pediatr. 2017 Feb;181:248-253.e3. PMCID: PMC5274603.
- Shepherd JA, Ng BK, Sommer MJ, Heymsfield SB. Body composition by DXA. Bone. 2017 Nov;104:101–105. PMCID: PMC5659281.
- Shepherd JA, Ng BK, Fan B, Schwartz AV, Cawthon P, Cummings SR, Kritchevsky S, Nevitt M, Santanasto A, Cootes TF. Modeling the shape and composition of the human body using dual energy X-ray absorptiometry images. PLoS One. 2017;12(4):e0175857. PMCID: PMC5397033.
- Shepherd JA, Fan B, Lu Y, Wu XP, Wacker WK, Ergun DL, Levine MA. A multinational study to develop universal standardization of whole-body bone density and composition using GE Healthcare Lunar and Hologic DXA systems. J Bone Miner Res. 2012 Oct;27(10):2208–2216. PMID: 22623101.
Recent Grants
- NIH/NCI 03/06/13 - 02/28/19. Lesion Composition and Quantitative Imaging Analysis on Breast Cancer Diagnosis.
- NIH/NIDDK 5/15/16 - 4/30/21. Optical Body Composition and Health Assessment.
- NIH/NIDDK 10/1/2016 - 9/30/2021. Shape Up! Kids.
- NIH/NIEHS 9/30/15 – 6/30/20. Environmental Chemicals and Postpubertal Breast Composition in a Latino Cohort.
- CDC 05/21/18 – 05/20/19. Dual Energy X-ray Absorptiometry (DXA) Scan Analysis and Quality Control Review for NHANES 2018-2022.
- General Electric 08/1/18 – 07/31/20. Quantitative Tomosynthesis Imaging
- NIH/NAIAD 06/29/06 – 11/30/20. LOC-IMPAACT Leadership Group.
- Shepherd and Steve Cummings, Co-PIs. Sutter Health/California Medical Center Research Institute "Deep Learning and Total Body DXA Scans (The TBDXA.I. Project)" 2019 - 2020
- Shepherd, Project Investigator. Centers for Disease Control and Prevention. Funded through the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) 75N95019C00024. "DXA Body Composition and Bone Mineral Density Review and Analyses for HANDLS" 8/12/2019 – 8/11/2023
- Shepherd and Peter Sadowski, Co-PIs; Donoviel, PI. National Cancer Institute, Translational Research Institute for Space Health (TRISH) NNX16A069A "Space-Feasible Body Composition and Body Shape Analysis for Long Duration Missions (Astro3DO)" 9/1/2019 – 8/31/2020
- Shepherd, Principal Investigator. Hologic, Inc. Hologic Agreement “Advanced 4C models for Adiposity and Function Biomarkers of Cancer Risk and Athletic Performance” 12/1/2018 – 5/31/2019
Current Graduate Students
- Jonathan Bennett, PhD in Nutrition (Chair). Title: Assessment of Hydration via Five Compartment Body Composition Methods.
- Dustin Valdez, PhD in Nutrition (Chair). Title: Evaluating Portable Breast Cancer Screening Technology for Women in the Pacific.
- Michael Wong, PhD in Nutrition (Chair). Title: Using 3D Optical Body Shape to Determine Various Health Indices.
- Lambert Leong, PhD in Molecular Biosciences and Bioengineering (Chair). Title: Using machine learning and deep learning to reduce the burden of cancer in Hawai‘i and the Pacific.
- Devon Cataldi, PhD in Kinesiology (Chair). Title: 4-Component Body Composition Models with Varying Body Fatness and Hydration: The Dakine Study
- Michael Omori, MS in Information and Computer Sciences. Title: The Development of a Body Composition Imaging System Using 3D Depth Sensors Utilizing Machine Learning for Testing in Microgravity Simulations
- Rosa Consuelo Villegas Valle, PhD in Nutrition (University of Sonora, Mexico) (Chair). Title: Tejido Adiposo Visceral (TAV) en Adultos Hispanos y su Relación con Alteraciones Cardiometabólicas
- Shane Spencer, MS in Electrical Engineering. Title: Applications of Deep Learning Techniques in the Systematic Melanoma Assessment and Risk Triaging (SMART) Pilot Study