AUTOMATION OF GENETIC-LINKAGE ANALYSIS USING FLUORESCENT MICROSATELLITE MARKERS

Automation of the typing of genetic markers offers advantages of speed , accuracy, and cost in the mapping of genetic traits and the construc tion of high-resolution linkage maps. We have developed an automated l inkage analysis system by (i) using a robotic pipettor to set up polym erase chain reactions (PCR) to amplify microsatellites with incorporat ion of a single fluorescent label; (ii) using an automated sequencing apparatus for detection of the PCR products; (iii) sizing alleles auto matically by the use of internal and external standards; (iv) iterativ ely filtering out nonallelic fragments and checking for Mendelian cons istency; (v) calculating the probabilities of selected genotypes; and (vi) automatically formatting the results for input to linkage analysi s programs. The method provides accurate sizing of alleles, minimizes the risk of error during manual reading and transcription of data, and increases the throughput of reliable data. It brings any inconsistenc ies or ambiguities in the data to the attention of the user and facili tates examination of the raw data, The ALF/ALP system, together with n ew, optimized microsatellite sets, particularly tetranucleotide repeat s, is likely to be well-suited to fully automatic genetic linkage anal ysis. (C) 1994 Academic Press, Inc.