Thoughts and a few refs about rare variants including their detection via sequence data 
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Questions:
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Biology/biochemistry:
   What are the basic principles behind sequencing?
   What are the tradeoffs between quality, quantity and cost?

Technology:
   How does one produce sequence information?            
   How does one align sequences?
   Different current generation options

Next-generation sequencing:  (Kidd ref from Sarah, thanks!)

Alkan, Kidd, et al. et Eichler (2009)
Personalized copy number and segmental duplication maps using
next-generation sequencing.
Nat Genet 41; (Oct 2009);  1061-1068.


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Methods:

Li BS and Leal SM (2008) Methods for detecting associations with 
rare variants for common diseases: Application to analysis of 
sequence data. American Journal of Human Genetics 83:311-321.

Morris AP and Zeggini E (2010) An Evaluation of Statistical 
Approaches to Rare Variant Analysis in Genetic Association Studies. 
Genetic Epidemiology 34:188-193.

Li BS and Leal SM (2009) Discovery of rare variants via sequencing:
implications for the design of complex trait association studies.
PLOS Genetics 5(5):e1000481.

Tavtigian SV et al (2008) Classification of rare missense 
substitutions, using risk surfaces, with genetic- and 
molecular-epidemiology applications. Human Mutation 29(11):1342-1354.

Goldgar de et al (2008) Genetic evidence and integration of various
data sources for classifying uncertain variants into a single
model. Human Mutation 29(11):1265-1272.

Madsen BE and Browning SR (2009) A groupwise association test for
rare mutations using a weighted sum statistic. PLOS Genetics
5(2):e1000384.

Dickson SP et al (2010) Rare variants create synthetic genome-wide
associations. PLOS Biology 8(1):e1000294.

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Population-genetics and disease assoc refs 

Scherer et al. Challenges and standards in integrating surveys of
structural variation. Nat Genet 2007

McCarroll et al. Copy-number variation and association studies of human
disease. Nat Genet 2007

McCarroll Extending genome-wide association studies to copy-number
variation. Human Molecular Genetics 2008

Itsara et al. Population Analysis of Large Copy Number Variants and
Hotspots of Human Genetic Disease. AJHG 2009

Auton et al (2009) Global distribution of genomic diversity
underscores rich complex history of continental human populations.
Genome Research 19(5):795-803.

Ionita-Laza I et al (2009) Estimating the number of unseen variants
in the human genome.  PNAS 106(13):5008-5013.

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Applications:

Hedges D et al (2009) Exome sequencing of a multigenerational human
pedigree. PLOS One. 4(12):e8232.

Ng SB et al (2009) Targeted capture and massively parallel sequencing 
of 12 human exomes. Nature 461:7261-U153.

Ng SB et al (2010) Exome sequencing identifies the cause of a mendelian 
disorder. Nature Genetics 42:30-U41.

Lupski JR et al (2010) Whole-Genome Sequencing in a Patient with 
Charcot-Marie-Tooth Neuropathy. New England Journal of Medicine. 
Mar 10 [Epub ahead of print]

Roach JC et al (2010) Analysis of Genetic Inheritance in a Family 
Quartet by Whole-Genome Sequencing. Science. Mar 10 [Epub ahead of print]

Cohen et al (2004) Multiple rare alleles contribute to low plasma levels of 
HDL cholesterol. Science 305:869-872.