Method for identifying clusters of fluorescence-activated cell sorting data points

Patent metadata

Field	Value
Publication number	US-9552416-B2
Application number	US-201313886932-A
Country	US
Kind code	B2
Filing date	May 3, 2013
Priority date	Apr 25, 2003
Publication date	Jan 24, 2017
Grant date	Jan 24, 2017

Abstract

A method and/or system for analyzing data using population clustering through density based merging.

First claim

What is claimed:

1. A method executed by a computer processor for identifying clusters of fluorescence-activated cell sorting (FACS) data points associated with one or more light intensity values measured for a particular cell, a group of cells, a sample of cells or a combination thereof comprising:
(A) constructing a normalized lattice L in d dimensions, wherein said lattice has an equal number of intervals in all directions and consists of M intervals in each direction, where M is a positive integer that defines Md lattice points, by
(i) setting size of a d dimensional unit area or volume to be Δ j in accordance with the formula Δ j =(max i x ij −min i x ij )/(M−1), j=1, . . . , d,
(ii) defining jth coordinate of lattice points y (m1, . . . ,md) to be y mj =min i x ij +(m j −1)Δ j , mj=1, . . . , M, and
(iii) defining lattice L as L={y (m1, . . . ,md) :(m 1 , . . . , m d )∈{1, . . . , M} d ;

(B) calculating weights for said lattice points using one or more of said data points according to a weighting rule in accordance with formula:

w
m

=

∑

i
=
1

n

⁢

⁢

∏

j
=
1

d

⁢

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max
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(

0
,

1
-



x

i
,
j

-

y
mj



/

Δ
j

)

,

 where w m is weight, y m is each lattice point and x i is one or more observed data points;
(C) determining a density at said lattice points relating a weight at a lattice point to weights at nearby lattice points using a density function, wherein determining the density includes computing an estimate of a density surface {circumflex over (f)}(y m ) wherein the Gaussian kernel is denoted by φ(b)=1/√{square root over (2)}πexp(−b 2 /2) and the estimated density y m is computed by formula:

f
^

⁡

(

y
m

)

=

1
/
n

⁢

∑

l
1

=

-

Z
1

Z
1

⁢

⁢

…
⁢

⁢

∑

l
d

=

-

Z
d

Z
d

⁢

⁢

ω

m
-
1

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∏

j
=
1

d

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ϕ
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(

l
j

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Δ
j

/

h
j

)

Assignees

• Univ Leland Stanford Junior

Inventors

• Walther Guenther
• Belitskaya-Levy Ilana
• Pan Jinhui
• Herzenberg Leonore A
• Moore Wayne
• Parks David

Classifications

• G06F17/30943

  Physics · mapped topic

• G06F17/30705

  Physics · mapped topic

• G06F17/3071 Primary

  Physics · mapped topic

• G16B5/00

  ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks · CPC title

• G06F16/35 Primary

  Clustering; Classification · CPC title