Indels Insertiondeletion Polymorphisms

Another form of a bi-allelic (or di-allelic) polymorphism is an insertion-deletion or indel. An indel can be the insertion or deletion of a segment of DNA ranging from one nucleotide to hundreds of nucleotides (such as is seen with an Alu insertion). The two alleles for di-allelic indels can simply be classified as 'short' and 'long'. From a certain perspective, STR markers can be thought of as multi-allelic indels since the different alleles are typically insertions or deletions of a tandem repeat unit.

Most di-allelic indels exhibit allele-length differences of only a few nucleotides. James Weber and colleagues at the Marshfield Medical Research Foundation recently characterized over 2000 bi-allelic indels in the human genome (Weber et al. 2002). A total of 71% of these indels possessed 2-, 3-, or 4-nucleotide length differences with only 4% having greater than a 16-nucleotide length difference. Allele frequencies for the short and long alleles have been measured in African, European, Japanese, and Native American populations (Weber et al. 2002). These markers can be easily typed and may prove useful for future genetic studies including human identity testing.


1. Why are SNPs being considered for use in human identity testing?

2. What are the advantages and disadvantages of SNPs compared to currently used STR markers?

3. Will SNPs replace STRs as a primary means of forensic DNA testing? Why or why not?

4. Are there ethical challenges with using SNPs to predict ethnicity and physical traits? If so, what are they and how should the law enforcement community use this type of information in the future?


Ahmadian, A., Gharizadeh, B., Gustafsson, A.C., Sterky, F., Nyren, P., Uhlen, M. and Lundeberg, J. (2000) Analytical Biochemistry, 280, 103-110.

Andreasson, H., Asp, A., Alderborn, A., Gyllensten, U. and Allen, M. (2002) Biotechniques, 32, 124-133.

Armstrong, B., Stewart, M. and Mazumder, A. (2000) Cytometry, 40, 102-108.

Bamshad, M.J., Wooding, S., Watkins, W.S., Ostler, C.T., Batzer, M.A. and Jorde, L.B. (2003) American Journal of Human Genetics, 72, 578-589.

Batzer, M.A. and Deininger, P.L. (1991) Genomics, 9, 481-487.

Batzer, M., Alegria-Hartman, M., Bazan, H., Kass, D.H., Shaikh, T.H., Novick, G.E., loannou, P.A., Boudreau, D.A., Scheer, W.D., Herrera, R.J., Stoneking, M. and Deininger, P.L. (1993) Fourth International Symposium on Human Identification, pp. 49-57. Madison, Wisconsin: Promega Corporation.

Bell, P.A., Chaturvedi, S., Gelfand, C.A., Huang, C.Y., Kochersperger, M., Kopla, R., Modica, F., Pohl, M., Varde, S., Zhao, R., Zhao, X., Boyce-Jacino, M.T. and Yassen, A. (2002) Biotechniques, Suppl, 70-77.

Berger, B., Holzl, G., Oberacher, H., Niederstatter, H., Huber, C.G. and Parson, W. (2002) Journal of Chromatography B Analytical Technology in Biomedical Life Sciences, 782, 89-97.

Blondal, T., Waage, B.G., Smarason, S.V., Jonsson, F., Fjalldal, S.B., Stefansson, K., Gulcher, J. and Smith, A.V. (2003) Nucleic Acids Research, 31, e155.

Bray, M.S., Boerwinkle, E. and Doris, P.A. (2001) Human Mutation, 17, 296-304.

Broude, N.E., Driscoll, K. and Cantor, C.R. (2001) Antisense Nucleic Acid Drug Development, 11, 327-332.

Budowle, B., Koons, B.W. and Errera, J.D. (1996) Journal of Forensic Sciences, 41, 660-663.

Budowle, B., Planz, J.V., Campbell, R.S. and Eisenberg, A.J. (2004) Forensic Science Review, 16, 21-36.

Butler, J.M., Shen, Y. and McCord, B.R. (2003) Journal of Forensic Sciences, 48, 1054-1064.

Callinan, P.A., Hedges, D.J., Salem, A.H., Xing, J., Walker, J.A., Garber, R.K., Watkins, W.S., Bamshad, M.J., Jorde, L.B. and Batzer, M.A. (2003) Gene, 317, 103-110.

Chakraborty, R., Stivers, D.N., Su, B., Zhong, Y. and Budowle, B. (1999) Electrophoresis, 20, 1682-1696.

Chen, X., Levine, L. and Kwok, P.-Y. (1999) Genome Research, 9, 492-498.

Dean, F.B., Hosono, S., Fang, L., Wu, X., Faruqi, A.F., Bray-Ward, P., Sun, Z., Zong, Q., Du, Y., Du, J., Driscoll, M., Song, W., Kingsmore, S.F., Egholm, M. and Lasken, R.S. (2002) Proceedings of the National Academy of Sciences USA, 99, 5261-5266.

Delahunty, C., Ankener, W., Deng, Q., Eng, J. and Nickerson, D.A. (1996) American Journal of Human Genetics, 58, 1239-1246.

Egeland, T., Dalen, I. and Mostad, P.F. (2003) International Journal of Legal Medicine, 117, 271-275.

Eng, B., Ainsworth, P. and Waye, J.S. (1994) Journal of Forensic Sciences, 39, 1356-1359.

Frudakis, T., Venkateswarlu, K., Thomas, M.J., Gaskin, Z., Ginjupalli, S., Gunturi, S.,

Ponnuswamy, V., Natarajan, S. and Nachimuthu, P.K. (2003a) Journal of Forensic Sciences, 48, 771-782.

Frudakis, T., Thomas, M., Gaskin, Z., Venkateswarlu, K., Chandra, K.S., Ginjupalli, S., Gunturi, S., Natrajan, S., Ponnuswamy, V.K. and Ponnuswamy, K.N. (2003b) Genetics, 165, 2071-2083.

Germer, S. and Higuchi, R. (1999) Genome Research, 9, 72-78.

Gibbs, R.A., Belmont, J.W., Hardenbol, P., Willis, T.D., Yu, F., Yang, H., Ch'ang, L.Y., Huang, W., Liu, B., Shen, Y., Tam, P.K., Tsui, L.C., Waye, M.M., Wong, J.T., Zeng, C., Zhang, Q., Chee, M.S., Galver, L.M., Kruglyak, S., Murray, S.S., Oliphant, A.R., Montpetit, A., Hudson, T.J., Chagnon, F., Ferretti, V., Leboeuf, M., Phillips, M.S., Verner, A., Kwok, P.Y., Duan, S., Lind, D.L., Miller, R.D., Rice, J.P., Saccone, N.L., Taillon-Miller, P., Xiao, M., Nakamura, Y., Sekine, A., Sorimachi, K., Tanaka, T., Tanaka, Y., Tsunoda, T., Yoshino, E., Bentley, D.R., Deloukas, P., Hunt, S., Powell, D., Altshuler, D., Gabriel, S.B., Zhang, H., Matsuda, I., Fukushima, Y., Macer, D.R., Suda, E., Rotimi, C.N., Adebamowo, C.A., Aniagwu, T., Marshall, P.A., Matthew, O., Nkwodimmah, C., Royal, C.D., Leppert, M.F., Dixon, M., Stein, L.D., Cunningham, F., Kanani, A., Thorisson, G.A., Chakravarti, A., Chen, P.E., Cutler, D.J., Kashuk, C.S., Donnelly, P., Marchini, J., McVean, G.A., Myers, S.R., Cardon, L.R., Abecasis, G.R., Morris, A., Weir, B.S., Mullikin, J.C., Sherry, S.T., Feolo, M., Altshuler, D., Daly, M.J., Schaffner, S.F., Qiu, R., Kent, A., Dunston, G.M., Kato, K., Niikawa, N., Knoppers, B.M., Foster, M.W., Clayton, E.W., Wang, V.O., Watkin, J., Gibbs, R.A., Belmont, J.W., Sodergren, E., Weinstock, G.M., Wilson, R.K., Fulton, L.L., Rogers, J., Birren, B.W., Han, H., Wang, H., Godbout, M., Wallenburg, J.C., L'Archeveque, P., Bellemare, G., Todani, K., Fujita, T., Tanaka, S., Holden, A.L., Lai, E.H., Collins, F.S., Brooks, L.D., McEwen, J.E., Guyer, M.S., Jordan, E., Peterson, J.L., Spiegel, J., Sung, L.M., Zacharia, L.F., Kennedy, K., Dunn, M.G., Seabrook, R., Shillito, M., Skene, B., Stewart, J.G., Valle, D.L., Jorde, L.B., Belmont, J.W., Chakravarti, A., Cho, M.K., Duster, T., Foster, M.W., Jasperse, M., Knoppers, B.M., Kwok, P.Y., Licinio, J., Long, J.C., Marshall, P.A., Ossorio, P.N., Wang, V.O., Rotimi, C.N., Royal, C.D., Spallone, P., Terry, S.F., Lander, E.S., Lai, E.H., Nickerson, D.A., Altshuler, D., Bentley, D.R., Boehnke, M., Cardon, L.R., Daly, M.J., Deloukas, P., Douglas, J.A., Gabriel, S.B., Hudson, R.R., Hudson, T.J., Kruglyak, L., Kwok, P.Y., Nakamura, Y., Nussbaum, R.L., Royal, C.D., Schaffner, S.F., Sherry, S.T., Stein, L.D. and Tanaka, T. (2003) Nature, 426, 789-796.

Giesendorf, B.A.J., Vet, J.A.M., Tyagi, S., Mensink, E.J.M.G., Trijbels, F.J.M. and Blom, H.J. (1998) Clinical Chemistry, 44, 482-486.

Gill, P. (2001) International Journal of Legal Medicine, 114, 204-210.

Gill, P., Werrett, D.J., Budowle, B. and Guerreri, R. (2004) Science and Justice, 44, 51-53.

Gilles, P.N., Wu, D.J., Foster, C.B., Dillon, P.J. and Chanock, S.J. (1999) Nature Biotechnology, 17, 365-370.

Grimes, E.A., Noake, P.J., Dixon, L. and Urquhart, A. (2001) Forensic Science International, 122, 124-129.

Haff, L.A. and Smirnov, I.P. (1997) Genome Research, 7, 378-388.

Hecker, K.H., Taylor, P.D. and Gjerde, D.T. (1999) Analytical Biochemistry, 272, 156-164.

Hedges, D.J., Walker, J.A., Callinan, P.A., Shewale, J.G., Sinha, S.K. and Batzer, M.A. (2003) Analytical Biochemistry, 312, 77-79.

Heller, M.J., Forster, A.H. and Tu, E. (2000) Electrophoresis, 21, 157-164.

Holden, A.L. (2002) Biotechniques, Suppl, 22-26.

Hosono, S., Faruqi, A.F., Dean, F.B., Du, Y., Sun, Z., Wu, X., Du, J., Kingsmore, S.F., Egholm, M. and Lasken, R.S. (2003) Genome Research, 13, 954-964.

Jobling, M.A. (2001) Forensic Science International, 118, 158-162.

Jurinke, C., Van Den, B.D., Cantor, C.R. and Koster, H. (2002) Advances in Biochemical and Engineering Biotechnology, 77, 57-74.

Kwok, P.-K., Carlson, C., Yager, T.D., Ankener, W. and Nickerson, D.A. (1994) Genomics, 23, 138-144.

Kwok, P.Y. (2001) Annual Reviews in Genomics and Human Genetics, 2, 235-258.

Lareu, M., Puente, J., Sobrino, B., Quintans, B., Brion, M. and Carracedo, A. (2001) Forensic Science International, 118, 163-168.

Li, J., Butler, J.M., Tan, Y., Lin, H., Royer, S., Ohler, L., Shaler, T.A., Hunter, J.M., Pollart, D.J., Monforte, J.A. and Becker, C.H. (1999) Electrophoresis, 20, 1258-1265.

Lovmar, L., Fredriksson, M., Liljedahl, U., Sigurdsson, S. and Syvanen, A.C. (2003) Nucleic Acids Research, 31, e129.

Lowe, A.L., Urquhart, A., Foreman, L.A. and Evett, I.W. (2001) Forensic Science International, 119, 17-22.

Marth, G., Schuler, G., Yeh, R., Davenport, R., Agarwala, R., Church, D., Wheelan, S., Baker, J., Ward, M., Kholodov, M., Phan, L., Czabarka, E., Murvai, J., Cutler, D., Wooding, S., Rogers, A., Chakravarti, A., Harpending, H.C., Kwok, P.Y. and Sherry, S.T. (2003) Proceedings of the National Academy of Sciences USA, 100, 376-381.

Morley, J.M., Bark, J.E., Evans, C.E., Perry, J.G., Hewitt, C.A. and Tully, G. (1999) International Journal of Legal Medicine, 112, 241-248.

Nikiforov, T.T., Rendle, R.B., Goelet, P., Rogers, Y-H., Kotewicz, M.L., Anderson, S., Trainor, G.L. and Knapp, M.R. (1994) Nucleic Acids Research, 22, 4167-4175.

Oliphant, A., Barker, D.L., Stuelpnagel, J.R. and Chee, M.S. (2002) Biotechniques, Suppl, 56-64.

Paracchini, S., Arredi, B., Chalk, R. and Tyler-Smith, C. (2002) Nucleic Acids Research, 30, e27.

Pastinen, T., Partanen, J. and Syvanen, A.C. (1996) Clinical Chemistry, 42, 1391-1397.

Phillips, C., Lareu, M., Sanchez, J., Brion, M., Sobrino, B., Morling, N., Schneider, P., Syndercombe Court, D. and Carracedo, A. (2004) Selecting single nucleotide polymorphisms for forensic applications. Progress in Forensic Genetics 10, ICS 1261, 18-20.

Primrose, S.B. (1998) Principles of Genome Analysis: A Guide to Mapping and Sequencing DNA from Different Organisms. Malden, Massachusetts: Blackwell Science.

Reynolds, R., Walker, K., Varlaro, J., Allen, M., Clark, E., Alavaren, M. and Erlich, H. (2000) Journal of Forensic Sciences, 45, 1210-1231.

Romualdi, C., Balding, D., Nasidze, I.S., Risch, G., Robichaux, M., Sherry, S.T., Stoneking, M., Batzer, M.A. and Barbujani, G. (2002) Genome Research, 12, 602-612.

Rowold, D.J. and Herrera, R.J. (2003) Forensic Science International, 133, 260-265.

Saiki, R.K., Walsh, P.S., Levenson, C.H. and Erlich, H.A. (1989) Proceedings of the National Academy of Sciences of the United States of America, 86, 6230-6234.

Sajantila, A. (1998) Second European Symposium on Human Identification, pp. 1-5. Madison, Wisconsin: Promega Corporation.

Sanchez, J.J., Borsting, C., Hallenberg, C., Buchard, A., Hernandez, A. and Morling, N. (2003) Forensic Science International, 137, 74-84.

Sapolsky, R.J., Hsie, L., Berno, A., Ghandour, G., Mittmann, M. and Fan, J.-B. (1999) Genetic Analysis, 14, 187-192.

Sherry, S.T., Ward, M.H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M. and Sirotkin, K. (2001) Nucleic Acids Research, 29, 308-311.

Shriver, M.D., Smith, M.W., Jin, L., Marcini, A., Akey, J.M., Deka, R. and Ferrell, R.E. (1997) American Journal of Human Genetics, 60, 957-964.

Shriver, M.D., Parra, E.J., Dios, S., Bonilla, C., Norton, H., Jovel, C., Pfaff, C., Jones, C., Massac, A., Cameron, N., Baron, A., Jackson, T., Argyropoulos, G., Jin, L., Hoggart, C.J., McKeigue, P.M. and Kittles, R.A. (2003) Human Genetics, 112, 387-399.

Sosnowski, R.G., Tu, E., Butler, W.F., O'Connell, J.P. and Heller, M.J. (1997a) Proceedings of the National Academy of Sciences USA, 94, 1119-1123.

Sosnowski, R.G., Canter, D., Duhon, M., Feng, L., Muralihar, M., Radtkey, R., O'Connell, J., Heller, M. and Nerenberg, M. (1997b) Proceedings of the Eighth International Symposium on Human Identification, pp. 119-125. Madison, Wisconsin: Promega Corporation.

Syvänen, A.C., Sajantila, A. and Lukka, M. (1993) American Journal of Human Genetics, 52, 46-59.

Syvänen, A.C. (2001) Nature Reviews Genetics, 2, 930-942.

Tapp, I., Malmberg, L., Rennel, E., Wik, M. and Syvanen, A.C. (2000) Biotechniques, 28, 732-738.

Taylor, J.D., Briley, D., Nguyen, Q., Long, K., lannone, M.A., Li, M.S., Ye, F., Afshari, A., Lai, E., Wagner, M., Chen, J. and Weiner, M.P. (2001) Biotechniques, 30, 661-669.

Tully, G., Sullivan, K.M., Nixon, P., Stones, R.E. and Gill, P. (1996) Genomics, 34, 107-113.

Vallone, P.M., Hamm, R.S., Coble, M.D., Butler, J.M. and Parsons, T.J. (2004) International Journal of Legal Medicine, 118, 147-157.

Walker, J.A., Kilroy, G.E., Xing, J., Shewale, J., Sinha, S.K. and Batzer, M.A. (2003a) Analytical Biochemistry, 315, 122-128.

Walker, J.A., Hughes, D.A., Anders, B.A., Shewale, J., Sinha, S.K. and Batzer, M.A. (2003b) Analytical Biochemistry, 316, 259-269.

Wang, D.G., Fan, J.-B., Siao, C.-J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J., Kruglyak, L., Stein, L., Hsie, L., Topaloglou, T., Hubbell, E., Robinson, E., Mittmann, M., Morris, M.S., Shen, N., Kilburn, D., Rioux, J., Nusbaum, C., Rozen, S., Hudson, T.J., Lipshutz, R., Chee, M. and Lander, E.S. (1998) Science, 280, 1077-1082.

Weber, J.L., David, D., Heil, J., Fan, Y., Zhao, C. and Marth, G. (2002) American Journal of Human Genetics, 71, 854-862.

White, L.D., Shumaker, J.M., Tollett, J.J. and Staub, R.W. (1998) Proceedings of the Ninth International Symposium on Human Identification. Madison, Wisconsin: Promega Corporation. Available online at:

Ye, J., Parra, E.J., Sosnoski, D.M., Hiester, K., Underhill, P.A. and Shriver, M.D. (2002) Journal of Forensic Sciences, 47, 593-600.

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