The Principles of Clinical Cytogenetics - Extra Materials - Springer

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Automation in the Cytogenetics Laboratory 125 FISH and Fluorescent Spot Counting Fluorescence in situ hybridization is based on fluorescently labeled probes that hybridize to unique DNA sequences along the chromosomes. There are many different applications of FISH; see Chapter 17 for more detail on this technology. Fluorescence in situ hybridization can be performed on either metaphase preparations or interphase cells. One of the applications is fluorescent spot counting used for translocation and copy number analysis performed on interphase cells (see Fig. 11). An example of an interphase FISH kit is the Vysis UroVysion ® kit for the detection of chromosomal abnormalities associated with the recurrence and progression of bladder cancer (see Chapter 17, Fig. 14). Generally, an imaging system for FISH needs to be able to capture low-light-level images, quantify the number of each fluorescent signal, and estimate the intensity ratio of the different signals. Because interphase cells are three-dimensional (3-D) structures, the fluorescent signals in interphase FISH and spot counting can be present in different focal planes. This means that to be able to see all signals, the user will need to focus on the different planes, making the presence of a motorized focus drive on an automated system imperative. The automated focusing allows for resolution of the multiple signals across a large focal depth. Images from different focal planes are captured, processed, and compiled into one pseudo-3-D image that shows all signals in focus. This 3-D image capture is often referred to as Z-stack. To visualize the different fluorochromes, the system uses different bandpass filters and a single, epi-illuminating light source (see Chapter 5, Fig. 3). An image is acquired for each fluorescent label used in the protocol, and the computer combines those into a color image. If the system is not equipped with an automated microscope with motorized filter block changing, a motorized filter wheel that will hold the different filters is highly desirable (5,6). (See Fig. 12.) The microscope focus, camera, and filter wheel are automatically controlled and synchronized by Z-stack software for multiplane, multicolor fluorescence image capture. Images in different focal planes are acquired and combined in a focused color image to ensure that faint signals that would otherwise be omitted are incorporated in subsequent analyses. To ensure consistent scoring and analysis of interphase FISH, the software should include the following: • Trainable classifiers to determine which cells to score, so users can “teach” the system to work with their own results and standards. • User-definable parameters to determine the scoring rules. Such parameters include spot size and spot separation distances (measured three dimensional) and the number of cells to score. • The ability to reprocess the images under different scoring rules without having to rescan the slide. • A reporting function that presents the results for review by the clinician. Reports should be customizable to reflect the user’s preferred data layout, and should include images of scored cells and different representations of the results, such as bar charts and scatter plots. M-FISH M-FISH, also referred to as multicolor FISH or multiplex FISH, can be viewed as fluorescent multicolor karyotyping and is mainly used for the detection and classification of interchromosomal aberrations (see Chapter 17). In this form of FISH, probes labeled with a combination of different fluors are hybridized with the chromosomes in a metaphase spread. Currently, 5 different fluorochromes are being used (7). The five different fluors give 31 (2n –1) color combinations, enough to uniquely identify the 24 different chromosomes in the human genome. However, lately it has been shown that the resolution of using a five-fluorochrome set is not high enough, and certain small aberrations might be missed (8). To improve resolution, a set of eight fluorochromes, to facilitate labeling each probe with a unique combination of two fluors, has been suggested. However, this would require nine filters (eight for the fluors and one for the DAPI counterstain) and would involve
126 Steven Gersen and Lotte Downey Fig 11. Software interface of a spot counting or interphase FISH system, showing thumbnails of cells and spots located by the system. (Courtesy of Applied Imaging.) some manual filter changing, as microscopes currently only accommodate eight-position filter wheels. Therefore, experiments with a seven-fluorochrome set have been performed, with promising results (8). From a hardware perspective, the requirements of an automated system for M-FISH are similar to the requirements of an automated system for interphase FISH: the system should include the fluorescent epi-illuminating light source and a filter wheel containing the appropriate filters. In addition, the system could include a metaphase finding capability as well as motorized focusing. The software for M-FISH (see Fig. 13) incorporates the following: • Sophisticated algorithms that analyze the images to determine the fluor combination a chromosome is labeled with and then assign a pseudocolor to each fluor combination. These pseudocolors should be user-changeable to improve visualization of rearranged chromosomes. • Karyotyping capabilities so that the colored chromosomes can be arranged in a karyotype (see Chapter 17, Fig. 17). • Individual pseudocolor display of a single chromosome to facilitate visualization of chromosomal aberrations. High-Resolution Comparative Genomic Hybridization and Microarray CGH The last forms of FISH discussed here are HR-CGH (high-resolution comparative genomic hybridization), and microarray CGH. Whereas M-FISH is a useful technique for determining inter-
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The Principles of Clinical Cytogene
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The Principles of Clinical Cytogene
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v Preface In the summer of 1989, on
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vii Preface to First Edition The st
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ix Contents Preface ...............
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Contributors SARAH HUTCHINGS CLARK,
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History of Clinical Cytogenetics 1
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4 Steven Gersen The hypotonic solut
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6 Steven Gersen marrow aspiration,
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8 Steven Gersen 9. Hsu, T.C. (1952)
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10 Martha Keagle Fig. 1. DNA struct
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12 Martha Keagle Fig. 3. Transcript
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14 Martha Keagle Fig. 5. Translatio
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16 Martha Keagle Fig. 7. The levels
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18 Martha Keagle single-copy DNA is
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20 Martha Keagle Fig. 10. Mitosis.
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22 Martha Keagle Fig. 11. Schematic
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24 Martha Keagle Fig. 13. Spermatog
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Human Chromosome Nomenclature 27 IN
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Human Chromosome Nomenclature 29 Fi
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Human Chromosome Nomenclature 33 Ta
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Human Chromosome Nomenclature 47 In
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Human Chromosome Nomenclature 49 Ma
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Human Chromosome Nomenclature 51 Un
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Human Chromosome Nomenclature 53 Ta
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Human Chromosome Nomenclature 55 46
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Human Chromosome Nomenclature 57 nu
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Basic Laboratory Procedures 59 II E
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Basic Laboratory Procedures 63 INTR
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Basic Laboratory Procedures 65 amni
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Basic Laboratory Procedures 67 Prep
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Basic Laboratory Procedures 69 Fig.
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Page 180 and 181: Structural Chromosome Rearrangement
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Structural Chromosome Rearrangement
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177 Prader-Willi Paternal deletion
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179 Table 2 Some Recurring Duplicat
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Sex Chromosomes and Sex Chromosome
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Cytogenetics of Infertility 247 INT
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Cytogenetics of Infertility 249 Amo
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Cytogenetics of Infertility 251 Tab
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Cytogenetics of Infertility 253 gen
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255 Primary ciliary dyskinesia Auto
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Cytogenetics of Infertility 257 cha
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Cytogenetics of Infertility 259 Tab
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Cytogenetics of Infertility 261 Fig
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Cytogenetics of Infertility 263 rat
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Cytogenetics of Infertility 265 39.
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268 Linda Marie Randolph By 1986, m
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270 Linda Marie Randolph Table 1 Ch
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272 Linda Marie Randolph Table 4 Th
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274 Linda Marie Randolph Table 6 Fr
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276 Linda Marie Randolph rate of 14
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278 Table 8 Outcome in Early (11-14
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280 Linda Marie Randolph Table 9 Vo
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282 Linda Marie Randolph In 1995, O
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284 Linda Marie Randolph Fig. 1. Il
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286 Linda Marie Randolph reported c
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288 Linda Marie Randolph The underl
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290 Linda Marie Randolph Fig. 3. Ul
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296 Linda Marie Randolph Fig. 6. De
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298 Linda Marie Randolph Choroid Pl
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300 Linda Marie Randolph Table 13 C
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302 Linda Marie Randolph Table 14 U
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304 Linda Marie Randolph then that
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306 Table 15 Prenatal Results for R
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308 Linda Marie Randolph Table 17 O
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310 Linda Marie Randolph DNA marker
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312 Linda Marie Randolph XX and XY
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314 Linda Marie Randolph 54. Simpso
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316 Linda Marie Randolph 116. Wang,
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318 Linda Marie Randolph 173. Cicer
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320 Linda Marie Randolph 232. Benn,
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Cytogenetics of Spontaneous Abortio
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348 Xiao-Xiang Zhang Fig. 1. An exa
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350 Xiao-Xiang Zhang cases availabl
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352 Xiao-Xiang Zhang Fig. 2. Metaph
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354 Xiao-Xiang Zhang patients, grea
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356 Xiao-Xiang Zhang Fig. 5. G-Band
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358 Xiao-Xiang Zhang Fig. 7. Sister
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360 Xiao-Xiang Zhang REFERENCES 1.
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Cytogenetics of Hematologic Neoplas
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387 Table 5 Association of Recurren
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389 del(8)(q22) t(8;16)(p11.2;p13)
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391 +17 -17 2° assoc. with +21 i(1
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Cytogenetics of Solid Tumors 421 IN
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423 Aytpical (see well-differentiat
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Cytogenetics of Solid Tumors 425 So
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Cytogenetics of Solid Tumors 427 ca
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Cytogenetics of Solid Tumors 429 do
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Cytogenetics of Solid Tumors 431 cl
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Cytogenetics of Solid Tumors 433 Fi
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Cytogenetics of Solid Tumors 439 no
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Cytogenetics of Solid Tumors 441 ch
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Cytogenetics of Solid Tumors 445 8.
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Cytogenetics of Solid Tumors 447 64
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454 Daynna Wolff and Stuart Schwart
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Fragile X 491 VI Beyond Chromosomes
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Fragile X 495 18 Fragile X From Cyt
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Fragile X 497 Fig. 1. Appearance of
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Fragile X 499 Table 4 Characteristi
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Fragile X 501 (KH domains) and clus
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Fragile X 503 have suggested differ
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Fragile X 505 The premutation form
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Fragile X 507 Table 4). FRAXE expan
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Fragile X 509 35. Heitz, D., Devys,
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Fragile X 511 93. Bennetto, L. and
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Fragile X 513 147. Oostra, B.A. and
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516 Jin-Chen Wang Fig. 1. Diagramma
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518 Jin-Chen Wang (50) and IGF2 (pa
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520 Jin-Chen Wang 3. Imprinting cer
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522 Jin-Chen Wang UNIPARENTAL DISOM
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524 Jin-Chen Wang Fig. 3. A diagram
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526 Jin-Chen Wang cause SRS (183).
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528 Jin-Chen Wang Studies comparing
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530 Jin-Chen Wang upd(21)pat Two ca
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532 Jin-Chen Wang 25. Ledbetter, D.
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534 Jin-Chen Wang 84. Bürger, J.,
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536 Jin-Chen Wang 138. Dryja, T.P.,
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538 Jin-Chen Wang 192. Karanjawala,
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540 Jin-Chen Wang 248. Creau-Goldbe
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542 Sarah Hutchings Clark condition
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544 Sarah Hutchings Clark the couns
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546 Sarah Hutchings Clark the coupl
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548 Sarah Hutchings Clark chromosom
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550 Sarah Hutchings Clark SMITH-MAG
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552 Sarah Hutchings Clark often at
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554 Sarah Hutchings Clark The relat
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556 Sarah Hutchings Clark Although,
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558 Sarah Hutchings Clark 33. Nicol
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560 Index Abnormalities, order of,
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562 Index Anus, imperforate, 310 AP
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564 Index CDK4, 394 CDK6, 396 CDKN2
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566 Index mosaicism, in amniotic fl
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568 Index Cutaneous anaplastic larg
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570 Index proximal 15q, 178, t179 p
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572 Index Folic acid pathway, 75 Fo
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574 Index Hereditary neuropathy wit
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576 Index Intrachromosomal recombin
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578 Index Male-specific region, Y c
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580 Index MTX, 76 Mucosa-associated
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582 Index Octamer, 14 Okazaki fragm
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584 Index Premature separation of s
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586 Index Recombinant chromosomes n
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588 Index Sézary syndrome (SS), t3
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590 Index t(4;14), 475 t(5;10), 375
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592 Index Treacher Collins syndrome
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594 Index Xq deletions, 225 Y trans
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596 Index XX males, 467, f468 and a
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