Statistical Genomics: LINKAGE, MAPPING, AND QTL ANALYSIS

Book Description

This handbook on the statistical issues of genomics covers current methods and the tried-and-true classical approaches, providing a complete picture of genome statistics. It contains much basic information on the use of statistics in genomics, including how to determine a sample size and carry out a hypothesis test. This volume is different from other statistics books on genetics in that it contains a mixture of discrete and continuous variables and larger amounts of data, describes the need for bioinformatics, and is computationally intensive. It also features software available on the Internet.

Customer Reviews:

statsitical genetics.......2003-12-23

There are many basic errors in statistics in this book, such as the concepts of expected value and degrees of freedom. The statistical background of the author should be very weak. From the bibliography (how many publications does the author have?) we can see whether the author is well prepared to write this kind of book. Did Dr. Ron Sederoff who wrote the foreword read the book thoroughly? If so, he should have pointed out those very obvious errors. Of course, Dr. Sederoff should not be responsible for those errors if he has no background in Statistics. I hope the author can check the book thoroughly before it goes to the fourth printing or just withdraw it from the publisher.

Beautiful job.......2002-06-15

The author of this book defines genomics as the study of whole genomes via the integration of cytology, Mendelian-quantitative-population-molecular genetics with bioinformatics and automated sequencing. It attempts to answer, the author states, such questions as to the physical and chemical requirements of genomes, the possible necessity that genes be located at certain sites to function normally, that particular DNA sequences and structures needed for gene functions, the total number of functional genes necessary for a biological system, and the homology between the DNA sequences of different species. He addresses the book to biologists interested in statistical issues in genomics, for mathematicians in genomics, and for students of genetics.

To satisfy these three classes of readers, she lists three different "tracks" for them consisting of a sequence of chapters recommended. Another good feature of the book is the inclusion of exercises at the end of each chapter, an absolute necessity for the understanding of this field. For those interested specifically in the efficacy of transgenic strategies in the design of viable breeds of plants and animals, this book will be helpful, for the author emphasizes in the book that the major application of genomics will be in finding optimal breeding strategies in agriculture and forestry.

After a brief introduction in chapter 1, the author outlines briefly Mendelian, population, quantitative, and molecular genetics in chapter 2, each presented as a separate discipline. The author never really defines what a gene "is" in the context of molecular genetics, as he does in the disciplines, but instead views it as a sequence of base pairs in the DNA strands, which has the potential of being expressed via transcription, RNA splicing, and translation, to a particular protein. Fortunately, in one of the exercises at the end of the chapter, the reader finds a connection between molecular and classical genetics by examining a trait (viewed as a simple compound) of a hypothetical plant.

Genomics as a discipline is introduced in chapter 3, and defined as the analysis of data from nuclear genomes, with the intent of learning about their structure, function, and evolution. Genome structure and sources of genome variation are discussed. Biological techniques in genomics are briefly discussed for interested readers. The author is careful to point out that complex traits cannot be related to the DNA sequences available currently as little is known about the molecular identity of most genes controlling these traits. Helpful diagrams are used to illustrate the important concepts, such as mating schemes, chromosome rearrangements, "natural" populations used in genomic research, RAPD, AFLP, and a diagram outlining the history of genetic markers.

Chapter 4 is a summary of the mathematical statistics needed in the book, but the author does give an example of the methods, dealing with mapping a gene for resistance to fusiform rust disease.

The statistical modeling of a single locus is carried out in chapter 5, as an example of what can be done, and as a warm-up for multiple locus models which follow later in the book. The author outlines how to detect segregation distortion using chi-square and log likelihood tests, and methods for determining sample size for marking screening using controlled crosses. The reader can get an idea of the importance of using PCR and RFLP to screen polymorphic genetic markers. A disequilibrium coefficient is defined and log likelihood methods are used to estimate it. Heterozygosity is defined in terms of allelic frequencies and estimated statistically. The author also details the use of Monte Carlo simulation to screen polymorphic markers.

In chapter 6, the author uses goodness of fit, likelihood ratio tests, and recombination fraction estimation to perform two-locus linkage analysis. Newton-Rhapson methods are used to solve the (non-linear) likelihood equations for obtaining maximum likelihood estimates. The author answers the question as to how large the sample size should be for detecting linkage, with the expected log likelihood ratio test statistic being the tool for the determination of this. This analysis is generalized to the more difficult case of natural populations in chapter 7. Linkage disequilibrium is then used in chapter 8 to also study two-locus models. The transmission/disequilibrium test and other tests are discussed in the light of finding markers linked to disease genes.

Linkage groups, defined as groups of loci inherited together according to statistical criteria, are studied in chapter 9. Locus ordering is considered and studied as a case, interestingly, of the traveling salesman problem, and some algorithms are proposed for its solution, such as seriation, simulated annealing, and branch-and-bound. But likelihood and bootstrap approaches are also discussed.

Multi-locus models and the important concept of map distance are considered in chapter 10. This chapter is the most interesting and helpful in the book, for it discusses in detail the relationship between multi-point map distance and physical distance. Morgan's, Haldane's, Kosambi's, and other map functions are discussed. Also, and most importantly, the quality of a genomic map is quantified, using the confidence of estimated locus order and locus distribution on the map.

The pooling or merging of linkage maps are considered in chapter 11, followed by the study of QTLs in chapter 12. Regression techniques are used for single-marker analysis and interval mappings are used to locate QTLs. QTL mappings for natural populations are discussed and the author considers the "statistical power" of QTL detection experiments. The question as to what QTLs really are is addressed, particularly the role of molecular biology and genomic mapping, and the limitations of QTL mapping. The author ends his discussion of QTLs by asking what would be the best approach for modeling a quantitative trait. A brief discussion of computer methods ends the book.

After finishing the book and noting the explosive influence of molecular biology, it is natural to ask: Will statistical methods in genomics fade away and be replaced by deterministic methods based on molecular and metabolic models?

One of the best books in Molecular Quantitative Genetics.......2000-04-03

The book discuses quantitative and population genetics on the bases of molecular level. It is very useful for genetic analysis across many disciplines, including plant and animal breeding, and human genetics. It provides useful explanations of some complex biometrical concepts.

A spetacular book.......2000-04-01

That is one of the big book in this area. That book is spetacular and very simple to understand.

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Packed with stunning photographs, easy-to-use maps, and all the information you really need to get the most from your visit! In this compact guide, our writers help you plan itineraries for short and longer stays. Complete with must-see sights on and off the beaten track as well as current hotel and restaurant recommendations. And the convenient size of the guide allows you to take it along in your pocket or handbag. Take the world in your pocket next time and travel with this handy Berlitz guide.

Berlitz Turkey Pocket Guide (Berlitz Pocket Guides)

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Turkey Berlitz Travel Guide comes complete with must-see sights on and off the beaten track as well as current hotel and restaurant recommendations. And the convenient size of the guide allows you to take it along in your pocket or handbag. Take the world in your pocket next time and travel with this handy Berlitz guide.

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In a flash, Valerie's world comes tumbling down. Talented pretty and popular. She was enjoying life and planing her future. She and Peter, the love of her life, were sharing their dreams. Now she and Peter share a problem...

Except it turns out to be Val's problem. Peter says he loves her, but he has to finish school, go to college, get on with his life. Valerie wishes she could get on with her life and her music career. But she lives each day with the reality Peter wants to forget -- and it is she who must make the impossible choices...When love has no answers.

Customer Reviews:

What Kind Of Love?.......2006-03-14

What kind of Love was a story based on a teenage pregnancy, and the responsibilities she would have to face. In this book the main characters were Valerie, her boyfriend Peter, and her best friend Carrie. Peter and Valerie were together for six months when she found out she was pregnant. They were scared to tell their parents because they were still kid them selves. They had no choice but to tell them. When Valerie tells her parents, they reply by telling her she has to have an abortion. When Peter tells his mom she states she is going to send him away to live with his father so he won't see Valerie or the baby.

According to my life, I can relate to Valerie's best friend Carrie. She is always giving Valerie good advice like I did when my aunt was pregnant. Carrie and I tell them, "It's not worth keeping the baby if the father left and you have no way to support the baby, unless if you get help." They wouldn't listen though. They think the father of the baby is going to come back for them. If the baby's father really liked you and was capable of being there for his child he would have never left. Valerie's boy friend Peter left without her knowing, but wrote to her when he got to his father's house in Chicago.

I really enjoyed this book a whole lot. One of my favorite parts was when Peter had left because when she found out she paid it no mind. She didn't care because she thought Peter was coming back and that they were going to move in together. She also thought they were going to get married. I think it was really silly because you really can't get married without parental consent.

My least favorite part was when Valerie actually found out Peter was playing games with her mind, he wasn't going to come back and she decided she was going to have the baby but put it up for adoption. I thought that was really depressing and emotional. It is hard to make decisions in a situation like this because you don't know if it would lead you the right or wrong way.

If you are a teenager who thinks they're in love and want to have a baby I recommend this book to you. This book makes you think twice. When you say you love someone you may think you do but it can be a lie. Like Valerie stated in the book "When you love someone you want to make them happy, but it takes two to do it." When you get with a guy get to know that person real well because that guy may only want one thing from a girl, get you pregnant then leave you like a bump on a log. Then you would realize it was a mistake. A mistake that will change your life forever and wouldn't be able to erase it ever again.

Bad Bad Book.......2006-02-28

This book is in one word awful. Val is portrayed as an idiot, thinking Peter was gunna marry her as a teenager. Peter is described as nothing more than a pushy sex fiend, well-off loser. Sheila Cole makes the book a cliffhanger; at least in Annie's baby (Beatrice Sparks) we knew what the final decision would be. The book is just terribly unrealistic, and I think that some of todays more impressionable teenage girls would get the wrong idea by reading this book, n then to make matters worse its so bad they probably wouldn't finish it so they wouldn't see how life ends up when the baby's daddy bolts for the exit. Read at your own risk!

Who would publish this?.......2006-01-23

This book was so... idiotic. Who would honestly not know they're pregnant for 4 months? Val is a girl that gets pregnant at 15 and thinks "Oh yea, I'm getting married." When her boyfriend's parents "force him" to go to a boarding school she's all crushed and says that they'll still get married. WHAT A JOKE! This book had to be one of the worst I've ever read, I mean what kind of teenage who's having unprotected sex think they won't get pregnant? My sister read this and hated it because it's poorly written! Who would publish this book? If you want a book to make fun of, pick up this book.

GREAT BOOK TO READ!!!!.......2004-02-26

It's a great book to read for a teenager. It teaches you to about the consequences of not using protection. I guess that the book caught my attention because I wondered what would happen if I were in that position. The author's writing style makes you want to keep reading the book and look for more of her books. I give it five starts because it was interesting, exciting and kind of sad.

wonderful.......2003-10-14

I was just roaming around looking for a good book to read when i fell across this one. The cover really got me interested, so i checked it out. Then i picked this for a report due in one of my classes. From the book, it made me feel like i was actually Valerie, living in her life and the different events she had to go through. But i thought it could have ended a lot of better. I mean she didn't even have the baby, and all she did was start to play the violin again. How boring... it should have ended with a big event even though thats suposed to be in the middle. And the biggest event that really happened was when Peter left her to go to college. And you know that if you were Peter you would have visited her, called her, sent her more letters, i mean for god sake, she's pregnant with his child! There was alot of things that seemed so unrealistic. But in spite of all the things that could have been done to make the book better i think it still was good, it made me think. Think about the exact sitation that could very well happen to me. I am 17, i have had sex, and after reading this book and hearing ohter stories about pregnant teenagers, it made me realise. At one point... theres no point in doing it at all. But once you've done it, you know you're going to do it again, and i talk from experience, and we're just soon to be adults trying to fit in, but still thats no excuse. Some teens just have sex because they hear about their friends doing it, or their so lonely and desperate for love they go to all the wrong places. For some advice wait until you're in love, then theirs meaning behind it all. And to parents, just because you hear of your kids having sex or are invovled with someone doesn't mean you have to punish them for trying new things, because sometimes your kids are well prepared enugh to stand up and face peir pressure, ecspecially when its a friend.But anyways, I'm getting off the main point - The book, Its well put together and interesting, and makes you think about what could really happen to a girl so innocent.

The Colors of Love: What Kind of Lover Are You..?

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The Colors of Love: What Kind of Lover Are You..?

Manufacturer: Bantam Books
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Binding: Paperback
ASIN: 0553105205

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What kind of lover are you..? Erotic, playful or constant? Find your own lifestyle with this provocative guide.

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What Kind of Love Did You Have In Mind?
Eric Folsom
Manufacturer: Wolsak and Wynn Publishers Ltd.
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What kind of love is this!: A story of adoption reconciliation

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What kind of Love is This
Sandra tells how adoption has affected her life in this book

What kind of love is this!: A story of adoption reconciliation
Sandra Kay Musser
Manufacturer: Jan Publications
ProductGroup: Book
Binding: Paperback

Customer Reviews:

What kind of Love is This.......2002-12-22

Musser states her viewpoints well. Her book made me feel that I was not alone. I'm glad it was available at the time I most needed it.

Sandra tells how adoption has affected her life in this book.......1998-06-14

Sandra Musser, founder of the Musser Foundation explores her adoption experience in a truthful and forceful method. A good read, when available.

What Kind of Love: Contemporary Christian Music CD

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Manufacturer: Allegis Publications
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What Kind of Love Is This?
Shawn And Mauldin Craig
Manufacturer: Allegis Publications
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What Kind of Love Is This
Sandra Musser , and Steve Ed. Zimmerman
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What Kind of Sex Education Is Appropriate for Teenagers? (Opposing Viewpoints Pamphlets Series)

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Editor Greenhaven Staff
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